The manufacturing error of spiral bevel gear tooth surface has a great influence on transmission efficiency and gear life. The error of the gear tooth surface needs to be measured accurately and fed back to the machine tool to adjust the parameters. When measuring the spiral bevel gear using a gear measuring machine, combined with the measurement theory of the tooth flank of spiral bevel gear, this paper proposed a method to compensate the inclination error in the measurement result precisely. Based on the iterative search method, a precision matching method for the theoretical and the measured tooth surface of the spiral bevel gear was designed to calculate the compensation results. The experimental results show that the inclination errors included in tooth surface measurement results reduced from more than 3 μm to less than 0.5 μm, and more than 70% of the errors are compensated by the proposed method. The accuracy of the measurement results improved significantly after compensation, and furthermore, it can provide a more accurate basis for the adjustment of machine tool parameters in the manufacturing process.