Phase unwrapping is used to establish the mapping relationship between camera and projector, which is one of the key technologies in fringe projection profilometry (FPP) based three-dimensional (3D) measurement. Although complementary Gray code assisted phase unwrapping technology can get a good result on the periodic boundary, it needs more coded images to obtain a high frequency fringe. Aiming at this problem, a complementary binary code assisted phase unwrapping method is proposed in this paper. According to the periodic consistency between the wrapping phase and binary codes, the coded patterns are generated. Then the connected domain strategy is performed to calculate the fringe orders using the positive and negative image binaryzation. To avoid the mistake near the periodic boundary, complementary binary code inspired by the complementary Gray code is proposed. The fringe order correction is also discussed for different situations in the first measured period. Only two binary images are needed in the proposed method,and the fringe frequency is not limited. Both the simulation and experiment have verified the feasibility of proposed method.