Traditional measurement method for face gear variations is time-consuming, for it is based on a complex procedure to establish the measurement coordinate system (MCS). Moreover, errors induced by misalignment between the design coordinate system (DCS) and the MCS are not properly processed in measurement. Therefore, this work proposes an efficient and accurate method to measure face gear flank variations using the coordinate measurement machine (CMM). Firstly, the MCS establishment without the need for an iterative process, which saves measurement time. Secondly, the measurement error compensation model (MECM) relies on the MCS and utilizes the four-parameter representation, which reduces variables in the nonlinear equation system. Finally, experiments demonstrated the effectiveness and repeatability of this method, successfully reducing misalignment errors. The tooth flank normal variation improved by 3.33%, the pitch variation improved by 26.28%, and the total cumulative pitch variation improved by 19%.