In order to meet demands of low noise and strong strength from their transmission of spiral bevel gears, loaded tooth contact analysis (LTCA) technique has become an increasingly access to determining the loaded tooth contact performances directly affecting the above demands. Moreover, the misalignment always is a main noise factor in the actual manufacturing and can directly affect the loaded tooth contact performances. Distinguish with the conventional simulated loaded tooth contact analysis (SLTCA) based on finite element simulation software package, a numerical loaded tooth contact analysis (NLTCA) method in consideration of the misalignments is presented for the spiral bevel gears. First, an improved computation model is established to perform the tooth contact analysis (TCA) considering the misalignments. Moreover, the principal curvature of contact points is also determined as the input for the proposed numerical LTCA. In the consideration of influences of the different misalignment, the loaded tooth contact performance items such as loaded contact force, loaded contact pattern, elastic contact deformation and loaded transmission error are calculated, respectively. Finally, the numerical instance including the results from SLTCA is given to verify the proposed method.