High resolution imaging in three dimension is important for biological research. RESOLFT (Reversible Saturable Optical Fluorescence Transitions) microscopy is one technique can achieve lateral super-resolution imaging. Twophoton microscopy naturally generate high resolution in the longitudinal direction with less background compared to single photon excitation. In this paper, we combine these two methods to realize three-dimensional high-resolution imaging. Spatial light modulator (SLM) is used as a flexible phase mask of the microscopy. Multiple super-resolution focuses as an array or in arbitrary positions could be generated by phase retrieval. This microscopy by SLM control could applied to parallel two-photon RESOLFT imaging or multiple spots tracking in high-resolution.