Multifocal structured illumination microscopy (MSIM) can achieve a doubled improvement in the resolution of the diffraction limit within an imaging depth of 50 μm. But when imaging thick samples, scattered light and defocused light limit its optical sectioning capability and image contrast. Two-photon MSIM (2P-MSIM) overcomes the influence of sample tissue scattering and further improves the imaging depth and imaging characteristics. However, the existing 2P-MSIM usually adopts galvanometer based scanning mirrors for precisely scanning imaging, which is a complicated and poor flexibility system. Here we propose a simpler 2P-MSIM. Two-photon multifocal scanning imaging can be realized by a spatial light modulator (SLM) with a high frame rate (< 845 Hz). The phase map of generating multi-focus array and linear phase grating loaded on the SLM simultaneously, high-precision parallel digital random address scanning and excitation imaging on the sample surface can be realized. The mechanical inertia problem of the galvanometer scanner in multifocal imaging can be solved by the proposed method while reducing the complexity of the system and improving flexibility. We finally realize two-photon multifocal imaging of mouse kidney tissue slices and lily of the valley rhizome by this system, which verifies the three-dimensional super-resolution imaging capability of this method. It is of great significance in developing the 2P-MSIM.