The 28-year-old third-seeded American served 23 aces and conceded just one break point in two sets, but he needed tiebreakers before he beat a brave Lu 7-6 (7-4) 7-6 (9-7).
The first set was even, with Isner serving strongly and Lu more than holding his own with his groundstrokes.
But once it came to the inevitable decider, Lu lost his first point on his serve and that was all Isner, the man with the second-best tiebreaker winning percentage in ATP tour history, needed to take the set.
Isner, ranked 14 in the world, dominated the first half of the second set, regularly winning service games to love and twice having the 62nd-ranked Lu at 0-40. But he failed to break both times, and the set again went to a decider.
Lu gave himself a chance by winning the first point in the second-set tiebreaker, but Isner pulled a point back and a Lu double-fault gave the American a match point on his serve.
Lu saved Isner's first match point with a backhand return winner from a second serve, and he saved a second on his serve, but a forehand volley into the net gave Isner a third chance and another unreturnable serve secured the match.
The victory reinforced Auckland as Isner's favourite tournament away from home: of his eight career titles, his only two away from the United States have been in Auckland.
Earlier, second seeds Julian Knowle of Austria and Marcelo Melo of Brazil upset the world's second best pair, Alexander Peya of Austria and Bruno Soares of Brazil, to win the doubles in a super tiebreak 4-6 6-3 10-5.