The nonparallel effects on the stability of the boundary layer flow was investigated using the Parabolie Stability Equations (PSE). In order to improve the accuracy of the calculation which is very important for the investigation of stability, higher order expansions in orthogonal functions in normal direction and the effective algebraic mapping to deal with the problem of infinite region were used and the way to collocate the boundary point based on its characteristics was adopted. With the effective control of step size in the marching procedure, the special condition was satisfied, and the stability of calculation was assured. From the curves of the neutral stability, the growth rate, the amplitude variation and disturbed velocity profile, the effects of the nonparallelism were given accurately and analyzed detailedly. It is found that the nonparallelism of the flow amplifies the amplitude and growth rate of disturbances, especially for three-dimensional disturbances, even can change the sign of flow stability from stability to instability for some cases. Computed results are in good agreement with the classical experimental results.