The Air Line Pilots Association struck United Airlines, the nation's largest, early this morning, but negotiations continued here.

Helen M. Witt, chairman of the National Mediation Board, said, "The strike has started but both sides do remain and are seeking an agreement." She said the talks would continue through the night.

Capt. Jim Waters, a pilots' spokesman in Chicago, said, "We are on strike. We have pickets up at all major locations."

Chuck Novak, a United spokesman, said early today that the airline will eliminate flights to 89 airports but continue serving 50, with emphasis on its flights at Chicago and Denver.

"In 72 hours we will assess our flight manpower resources and restore service to all cities as quickly as possible," he said. He recommended that passengers holding United tickets check with their travel agents to see if their United flight is operating. He said the airline has assigned extra staff at airports to help travelers find alternate bookings if necessary. today, a spokesman said.

In the prestrike deadline maneuvering, the Air Line Pilots Association (ALPA) charged United with a variety of unfair labor practices, including "threats, intimidation and bonus payments to replacements."

At a Tysons Corner, Va., hotel, 400 United pilots, other employes and family members counted down the last seconds before the strike was announced over live video hookup by union officials in Chicago.

The pilots applauded enthusiastically, but privately expressed anger and disappointment.

"To a man, we love this company," said Capt. Charles (Tex) Goppert, a United pilot and union representative based in Washington. "In 21 years with this company, I've never seen solidarity like this . . . . The company doesn't seem to be interested in anything except putting us on the street."

The central issue separating the two sides has been United's insistence on hiring new pilots for lower salaries than it pays its 4,900 pilots. ALPA has charged that two pay schedules would dilute the quality of pilots and divide the union. A spokesman said United will fly a "reduced schedule" using management pilots, not-yet-hired but already trained replacements and ALPA members who cross the picket lines. It was not clear if flight attendants and mechanics would continue to work.

For the short term, the strike is expected to bring chaos to the flying public. United schedules about 1,500 flights daily to 10 foreign destinations and 149 cities in all 50 states, and carries about 15 percent of U.S. air travelers.

The airline is particularly strong in Chicago, Denver, San Francisco, Los Angeles and Honolulu.

The airline has 34 flights a day to or from Washington National Airport, 26 a day at Washington Dulles International Airport and 10 a day at Baltimore-Washington International Airport. Most Washington-area service is oriented to Chicago, Denver and the West Coast.

Passengers holding United tickets will have to make arrangements with other airlines if United cancels their flights. Delta and American, two of United's major competitors, said they will provide confirmed reservations to those holding full-fare United tickets if space is available. Passengers holding United discount tickets will be accepted on a space-available or standby basis or can upgrade their tickets to full fare.

Continental Airlines said it will accept full-fare United tickets on a standby basis, but will not accept discounted United tickets.

Under airline deregulation, each airline can treat a United ticket as it wishes.

United says if necessary it will rebuild to its full schedule over a period of months with new hires.

The carrier has trained at least 500 pilots that it is ready to hire and has about 120 management pilots. Additionally, it has been advertising to hire qualified replacements at higher salaries than those paid by low-fare competitors such as Continental and People Express.

Negotiations resumed here Monday with Witt after a three-week hiatus. When talks resumed, United was offering to start newly hired second officers for $21,500 instead of the $22,452 it now pays.

The average United pilot is paid about $90,000 annually, the airline says, and the captain of a 747 jumbo jet receives about $150,000 annually. A two-tier pilots' pay schedule similar to the one United is seeking was negotiated in November 1983 by arch-rival American Airlines, whose pilots are represented by another union.

Industry observers believe that United needs a similar contract to remain competitive over the long run despite showing a record $564 million operating profit in 1984. During the first three months of this year, however, United reported a net loss of $661 million.