The relationship between system alignment errors and four equivalent misalignments was built through 3-D tolerances modeling theory and transfer matrix accumulating method based on feature variances. Tooth contact analysis algorithm with consideration of alignment errors was provided, and the contact pattern digital features were completely defined. In the situation of transmission performance requirements and cost constraints, the accuracy of parts was optimized based on genetic algorithms by using meshing relative to alignment errors sensitivity as the optimal objective function. Taking a pair of spiral bevel gears as an example, the feasibility of tolerance optimization method was verified by comparing the meshing and transmission errors before and after optimization.