The Synthetic Fuels Corp. yesterday announced the resignations of controversial former acting chairman John J. McAtee Jr. and two other holdovers from the Carter administration team, clearing the decks for a possible change in focus at the troubled organization.

McAtee, an energetic Wall Street attorney, said he was leaving in part because his management style is "not fully compatible" with that of Edward Noble, who was sworn in Wednesday as the corporation's new chairman.

"I came here to be the number two guy and to make deals in a Wall Street way, from the philosophy of a high-powered commercial banking institution," said McAtee, 44. "I'm not convinced Noble is committed to that kind of approach."

McAtee said his resignation was not related to controversy over his testimony recently before a House subcommittee that his $161,000 salary from the corporation -- which he has since voluntarily reduced to $69,500 -- was a hardship compared to his income at the law firm of Davis Polk. The environment, energy and natural resources subcommittee, chaired by Rep. Toby Moffett (D-Conn.), has recommended an overhaul of the compensation system at the corporation.

The corporation was set up last year to stimulate the infant synthetic fuels industry with $17.5 billion in loan guarantees, purchase commitments, price supports and loans, and is expected to be involved in delicate negotiations with teh 64 companies who have applied for some of that aid.

President Reagan recently fired the first chairman, John Sawhill, and the departure of McAtee, financial vice president Robert Blakely and project development chief Larry Lukens, who formally resigned in February, leaves Noble in full control.

Noble is "more project-oriented" than he is, McAtee said, and will operate somewhat more slowly than he would have. In addition, "Ed from day one has wanted [Victory] Shroeder," a 59-year-old Atlanta real estate developer, is his second-in-command, McAtee said. "That's an appropriate reason to have him."