Fringe projection profilometry is an efficient, fast and non-contact 3D measurement technique, widely used in industrial parts measurement. However, invalid phases are common when measuring step edges such as holes, ribs and steps in industrial parts which leads to outliers in reconstructed point cloud and ultimately causes reduction of valid point cloud and dimensional measurement errors. In this paper, an error compensation method on 3D measurement of step edge is proposed. 3D measurement space is firstly divided into multiple subspaces based on binocular camera system parameters. Then a calibration method is proposed to calculate the amount of compensation for each subspace and obtain parameters of edge error model. After calibration, point cloud of object with step edge is reconstructed by projecting phase-shifting structured light fringe patterns. By using Principal Component Analysis (PCA), normal estimation of point cloud is implemented. And edge feature is extracted with combination of eigenvalues variation of the covariance matrix and first-and second-order fitting based on two-dimensional projection. At the same time, the corresponding deviation amount of each edge point is solved on the basis of aforementioned edge error model. Finally, the accurate step edge is obtained after error compensation according to the normal direction and deviation amount. Experimental results show that, the method proposed can effectively improve the 3D measurement accuracy of step edge.