Boyd went 30-of-40 for 331 passing yards and added 28 more on the ground, but also fumbled twice for the Tigers (6-0, 4-0 ACC), who trailed until scoring a pair of quick TDs in the final quarter.
Sammy Watkins made seven catches, including a 49-yard scoring strike, en route to 102 yards and David Beasley returned a fumble for a TD as Clemson racked up its 14th win in 15 games going back to last season.
The Eagles (3-3, 1-2) were paced by Chase Rettig, who completed 13-of-21 for 193 yards, with one touchdown and an interception.
Alex Amidon led BC's receiving corps with six grabs for 122 yards, including a 69-yard score.
Swim Week Miami Beach 2014 [PHOTOS]