The misalignment errors of Hartmann-Shack (H-S) wavefront sensor and deformable mirror in adaptive optics system and Common Path/Common Mode adaptive optics system are studied, by using the directly wavefront slope method and the voltage-surface characteristic of deformable mirror. In the adaptive optics system, re-measurement of the deformable mirror′s response functions would decrease the effects of adjustment error and the system has large tolerance; while in the Common Path/Common Mode adaptive optics system, adjustment errors would have different effects on the compensation performance of the system, because different data fusion method is used. Modified slope fusion method and voltage fusion method have taken the difference of the matching relationships of two H-S sensors and deformable mirror into consideration, so the effects of adjustment errors are the same with those of the normal adaptive optics system. The systems have large tolerance too. Higher precision of adjustment is required when the diretly slope fusion method is used because it is base on the assumption that the relationships at two H-S sensors and deformable mirror are completely identical. The numerical results are given in the course of analyzing.