Lee (14-6) stroked a two-run, bases-loaded single to cap off a six-run third inning and also hit his first career triple in the fifth. Chase Utley, who also drove in four runs, hit a long three-run homer in the third.
On the mound, Lee allowed two runs while scattering eight hits and walking none, at one point retiring 11 straight en route to winning his fourth consecutive decision. The left-hander's 14 strikeouts marked his fourth double-digit strikeout game this year.
Lee is 4-0 with a 2.05 ERA in his last six starts and 5-1 with a 2.29 lifetime ERA against Miami. He's also a career .391 hitter against the Marlins.
Philadelphia has won six in a row over Miami.
In his first major-league start, Sam Dyson (0-1) allowed seven runs on six hits and three walks while striking out only one. He struggled to find control, with just 34 of 63 pitches going for strikes.
Utley got the Phillies started with an RBI groundout in the first. His 17th homer in the third gave them a four-run lead.
Later in the frame, Cody Asche drove in a run with a single to right field. Giancarlo Stanton's throw home was on the mark, but Marlins catcher Jeff Mathis couldn't handle it before being barreled over by Domonic Brown.
After Roger Bernadina drew a walk to load the bases, Lee singled to score two more and chase Dyson from the game. In all, 11 Phillies went to the plate in the inning.
Darin Ruf hit a two-run homer, his 14th of the season, in the sixth. He finished with two hits and three runs scored.
The Marlins' first run came in the fifth inning, when Adeiny Hechavarria singled to bring home Justin Ruggiano, who doubled. Ruggiano also had an RBI double in the sixth.
Christian Yelich, Stanton and Mathis each struck out three times.
The loss was Miami's ninth in 11 games.
NOTES: In their last 29 games against the Marlins, the Phillies are 22-7. ... Lee passed the 200-innings threshold for the sixth straight season, the fourth-longest active streak in the majors. He also reached 200 strikeouts for the third consecutive year. ... Dyson became the 12th different starting pitcher used by the Marlins this season, tied for most in the National League with the Mets and Pirates. ... The Phillies on Monday announced Carlos Arroyo as the team's new Minor League Pitching Coordinator. ... Tuesday, Roy Halladay (3-4, 7.28) starts for the Phillies, while Brian Flynn (0-1, 10.13) goes for the Marlins.