The chancellor of Bob Jones University has branded Secretary of State Alexander M. Haig Jr. a "monster in human flesh" and called on God to "smite him hip and thigh, bone and marrow, heart and lungs . . . and destroy him quickly and utterly."

Bob Jones Jr., chancellor of the fundamentalist South Carolina college, leveled the broadside after the State Department, for the second time in four months, refused to grant a visa to extremist Protestant leader the Rev. Ian Paisley of Northern Ireland.

Paisley is a member of the school's international board of trustees and had been invited to speak, as he has many times in the past, at its annual Bible Conference.

The State Department said yesterday it turned down Paisley's visa application because it remains "gravely concerned" over Paisley's "inflammatory actions and statements." A department spokesman had no comment on Jones' attacks on Haig.

Speaking to nearly 7,000 persons who gathered for the school's 55th annual Bible Conference, Jones called the visa denial "nothing but Catholic bigotry."

"I am going to pray that God will get rid of that man," Jones said of Haig at a Thursday chapel service. "I hope you will pray too that the Lord will smite him hip and thigh, bone and marrow, heart and lungs, and all there is to him, that He shall destroy him quickly and utterly.

"This man is a tyrant of the worst sort, a monster in human flesh and a demon-possessed instrument to destroy America," Jones continued. "Let's pray that God will remove him. God answers prayers."

Jones, who is the son of the school's founder, asked his listeners to write a letter to President Ronald Reagan, "telling him that as Americans we cannot tolerate this sort of tyranny." He also said Reagan should have fired Haig, "a man who has presidential ambitions," long ago, and that Reagan's failure to do so "shows how weak the president is and how under the influence he is of men who dominate him."

Paisley made his most recent visa application on March 19. The State Department said it turned him down for the same reason it revoked his visa last December, acting under a law that permits the exclusion of "those aliens whose activities in this country would be prejudicial to the public interest of the United States."

At the time of the December incident, Paisley, who is a member of the British Parliament, was seeking to make speeches here on behalf of the militant Protestant cause in Northern Ireland. He is an outspoken advocate of the use of force against the outlawed Irish Republican Army.

After the December revocation, Paisley's wife, Eileen, came to this country and delivered her husband's speech to the National Press Club.

On his March visa application, Paisley indicated he wanted to speak not as a political leader but in connection with his duties as head of the Free Presbyterian Church of Northern Ireland. The State Department was unmoved.

Bob Jones has been in the news on another front in recent months, helping to trigger a major civil rights controversy that wound up embarrassing the Reagan administration.

The school, along with Goldsboro (N.C.) Christian Schools, is asking the Supreme Court to grant it tax-exempt status despite the fact that it practices racial discrimination.

In January, the administration said it planned to give the schools their exemptions, reversing a 12-year-old government policy, but after the storm of protests that followed, it retreated and asked the courts to settle the matter. The case is pending.