In this paper, a deformable mirror is employed as a pupil filter in a super-resolution imaging system because it can be used to modulate optical field phase quickly and flexibly. The genetic algorithm is adopted to design pupil phase structures with different super-resolution parameters, and the closed-loop phase fitting of pupil filter is realized by modifying the closed-loop reference matrix of the adaptive optics system. On this basis, the experiments are conducted to compare the super-resolution imaging results with different pupil filter situations. The experimental results show that the deformable mirror can well fit the designed phase of pupil filter and the super-resolution imaging parameters are in agreement with theoretical predictions. The deformable mirror processes phase fitting of super-resolution pupil by employing reflective type and controlling mirror′s shape. This method has no requirement of polarization state of incident light, and it is in favor of practical application.