Phase encoding and phase-shift profilometry are two commonly used 3D measurement techniques. However, the acquired phases in the techniques are subject to jump errors due to phase ambiguity and phase errors caused by multiple heterodyne. The phase-shifting profilometry also makes the selection of fringe period difficult. To overcome this problem and achieve high-precision measurement, a phase unwrapping method that combines dual-frequency heterodyne with double complementary phase encoding is proposed. First, two wrapped phases are obtained by two groups of sinusoidal fringes; the heterodyne phase is obtained after heterodyne processing, and the high-frequency phase is expanded by heterodyne phase. Second, the fringe levels are obtained using the complementary phase encoding fringes that are shifted by half an order, and then the absolute phase is obtained by selecting different phase coding levels according to different regions for the first phase unwrapping; Finally, the phase noise is removed by exploiting the difference between the phase slopes of adjacent pixels. Experimental results show that a system with the proposed method achieves an RMS error of 0.015 mm. In addition, the period of dual-frequency heterodyne synthesis does not need to cover the whole field of view, which breaks the limitation of frequency selection of the traditional dual-frequency heterodyne method and triple frequency heterodyne method, enabling high-precision measurement with higher frequency fringes. This method overcomes the limitations of the phase principal value error when using higher frequency fringes for high-precision measurement, improves the measurement effect of reflective objects, and effectively avoids the error caused by phase jump.