Abstract The misalignment error between the gear theoretical coordinate system and actual gear coordinate system is illustrated, as well as its influence on the measurement of tooth surface deviation is discussed. On the analysis of the tooth convex and concave surface error measurement process, the measured points in the theoretical coordinate system are transformed from the actual measured points in the actual coordinate system. Then, an eight tooth-surface fitting method is utilized to calculate the misalignment error and the compensation method is given. Finally, actual measurements of three different spiral bevel gears are analyzed, and the misalignment error are calculated. Using the proposed compensation method, both the eccentricity and tilt are compensated to some extent. And the machining suggestions of each spiral bevel gear are also given according to its compensated tooth surface error distribution.