Would New York City's transit system by any other name still be the same confusing tangle of rail and bus lines in the eyes of the riders? The Metropolitan Transportation Authority thinks not, and it is spending $3 million to prove it.

Over the next four years, the authority plans to replace the myriad names and logos used by its five subsidiaries with a uniform M.T.A. logo and somewhat simpler names, though not necessarily shorter ones. The Metro-North Commuter Railroad, for instance, becomes the M.T.A. Metro-North Railroad, while the Metropolitan Suburban Bus Authority becomes M.T.A. Long Island Bus.

The idea, transit officials say, is to make it clear that every public bus, subway car and train in New York really belongs to the authority. If this sounds like a bureaucratic version of an identity crisis, it is. In essence, the M.T.A. feels misunderstood. Questions of Cost

"If you look at all of our vehicles there is no way of telling these vehicles are responsible to the same authority," said Alicia Martinez, the authority's marketing director. "How do we identify ourselves to customers so they know who is responsible for the system?"

Peter E. Stangl, the M.T.A. chairman, has said the new logo and simple names are part of a larger effort to weld the authority's rail and bus services, linking them with an electronic fare-collection system that someday will allow riders to transfer easily from one part of the system to another. He said that for a multi-billion-dollar agency, the cost was a modest price to clarify its services to riders.

"I want to convey that we are a regional transportation system, that each of the agencies are a part of a bigger system," Mr. Stangl said. "Frankly, it's about time we did something to stop confusing our customers."