When Ayatollah Ruhollah Khomeini returns to his home in this dusty town 90 miles south of Tehran, he will find an already established microcosm of his long-sought Islamic republic.

Nearly every vestige of the present central government has disappeared from Qom, a "holy city" revered by Shiite Moslems for its shrine to Fatemeh, considered one of the saints of the faith.

The city's government is effectively under the control of the local clergy. All the courts are closed, and an adhoc system of Islamic justice has taken their place. The regular police have given way to a corps of more than 500 unarmed "Islamic guards" identified by special badges who direct traffic and, in some cases, enforce the law.

Although this city of nearly half a million people is still technically under martial law, the troops and tanks that once controlled the streets pulled out in December, and the military regulations are no longer observed.

As in Qom, Khomeini supporters have started a gradual takeover of other Iranian cities and are reported to be in almost complete control of Isfahan, the country's second largest city, and of Shiraz.

The Qom office of the state power authority is on strike to protest the government in Tehran of Prime Minister Shahpour Bakhtiar, but workers from the department recently came to put up lights at Khomeini's house here.

A "Khomeini welcome committee" under a Qom clergyman, Mohammed Yazdi, runs a chain of cooperative shops to assure food distribution to the populace while many merchants and workers are on strike.

The committee has organized a general sprucing up of the brick house where Khomeini had been living when he was arrested 14 years ago and sent into exile by the government of Shah Mohammad Reza Pahlavi. Volunteer workers have been carrying out street repairs and other works around the house, and every day a steam roller smooths out a dirt alley running along one side of it.

No one pays any state taxes anymore, but residents say they will resume once an Islamic government takes power. The "religious taxes" that are traditionally paid to clerical leaders here have taken on a more important role, serving for welfare payments and a kind of strike fund in addition to financing two clergy-run hospitals and other services.

No one bothers to file complaints at the Qom police station anymore. Policemen still show up for work there, but they rarely do anything, much less try to put anyone in jail.

Even the local office of the oncedreaded secret police, SAVAK, is only a shadow of its former notoriety.

A British theological student who has embraced Islam and changed his name from John to Yahya Cooper, said he was summoned to the SAVAK headquarters three months ago, sat in a room without seeing anyone for two hours and was then told he could go.

"The normal police don't seem to be functioning" Cooper said. "They just come out and smile and direct traffic every once in awhile."

Cooper, who came here nine months ago to study Islamic teachings along with some 18,000 other students at the Qom Theological School, reputedly the largest such Shiite instrsution in the world, spends much of his time these days helping with translations at interviews with Ayatollah Kazem Shariatmadari, the leading resident religious figure in Qom.

With his curly red hair and beard, the lanky Cooper stands out from other theological students despite the full-length brown burnoose he wears over a corduroy suit. But he displays the same serenity and calm as Shariatmadari as he sits cross-legged on a Persian carpet at the ayatollah's interviews.

Although Shariatmadari has reservations about pressing ahead full-tilt with an Islamic republic and risking a confrontation with the army, he has issued an edict telling followers to form committees to run their affairs themselves in cities "where the police and the government are weak and cannot control the situation."

This is essentially what has happened in Qom. The Islamic justice system has not seen much use here, but recently "Islamic guards" apprehended a youthful thief and brought him to the house of the Khomeini Welcome Committee chief. His parents were summoned and took him home after he promised never to steal again.

In other cities that are already effectively under rule -- prematurely -- of the Islamic republic, punishments have been harsher.

In the northeastern holy city of Mashad, four men accused of stealing a car were arrested by Islamic security officials and sentenced by a clergyman to a public flogging of 25 lashes each. They were then released.

In the central city of Isfahan, a luckless American employed by Bell Helicopter International is to be tried twice for the same offense. The American, identified as Alfonso Durello, was fined $3,000 by an Islamic court after he shot and wounded a taxi driver Jan. 30. Durello was beaten by a crowd after the incident, then taken to a local ayatollah's house where he was detained.

According to Tehran newspapers, he was freed Tuesday after his conviction, but shortly afterward was arrested again by regular police.

The official law enforcement and judicial authorities are expected to regain their powers if Khomeini realizes his dream of establishing an Islamic republic in Iran. For now, however, the confusion created by his parallel "provisional government" is reflected in the not uncommon sight these days of a uniformed policeman and an "Islamic guard" directing traffic side by side.

Should Khomeini succeed, this Islamic stronghold stands to increase its stature. It is already the spiritual capital of the nascent Islamic republic.

If Khomeini returns to his modest one-story brick villa here in triumph after having prevailed in Tehran's battle of governments, Qom could become the new republic's de facto political capital as well.