The victory completed a domestic double for City after they secured their first Women's Super League title in 10 years under Andree Jeglertz.
Brighton, appearing in their first FA Cup final, started brightly but struggled to recover after falling behind.
Khadija Shaw gave City the lead in the 38th minute before Alex Greenwood doubled the advantage deep into first-half stoppage time.
The Jamaican international, who signed a new four-year deal earlier this week, opened the scoring by powering a header beyond Chiamaka Nnadozie from Greenwood's cross.
Nnadozie was then unable to keep out Greenwood's low free-kick as City took control before the break.
Brighton remained in the contest for long periods, but Aoba Fujino's strike midway through the second half put City firmly in control before Vivianne Miedema added a fourth late on.
The scoreline was emphatic, although the underlying numbers suggested a more competitive contest. However, City were far more clinical in front of goal.
Greenwood, who scored City's second goal and helped secure a clean sheet, was among the standout performers.
The result clinched FA Cup glory for Man City, their fourth time lifting the trophy, capping an impressive season with a domestic double.
