An approach is presented to detect and compensate position variation, which adopts complemented fringe projection technique. It can effectively solve the problem of measurement error aroused by inexact positioning in the in-line inspection. Firstly, complemented fringe relative to referenced sample are generated and projected onto its surface. Then the fringe pattern images are captured. Secondly, fringe analysis techniques are adopted to acquire the phase when referenced sample is perfect positioned; the same way is employed onto the product which is inaccurate positioning. The phase of non-distortion and overlap area are chosen to compute difference caused by the inexactly positioning. This phase differences are added to the absolute phase for referenced sample to obtain a new absolute phase after positioning error, 3D coordinate of actual product are acquired using phase and depth mapping relation. At last, position variations are computed by least squares overlap iteration, and the rigid transform is employed to compensate error. Simulation analysis and experimental results prove the validity and feasibility of the approach.