We present a method and a system of multifocal two-photon laser scanning microscopy (MTPLSM) based on double-helix point spread function (DH-PSF) engineering (DH-MTPLSM) to improve the imaging speed and resolution. In the excitation light path, a high-speed phase-only spatial light modulator (SLM) is employed to generate three-dimensional (3D) multifocal arrays and implement high-precision parallel digital addressing scanning of the sample surfaces. In the detection light path, a double-helix phase plate is inserted to modulate the system detection PSF to DH-PSF, which provides axial information of the sample. The aim is to reduce the number of layers scanned axially and ultimately enhance the speed of 3D imaging. Moreover, with a DH-PSF-based digital refocusing algorithm, we reconstruct the wide-field images of the sample at different depths and obtain the 3D optical sections of the sample by single 2D scanning. On this basis, we build a DH-MTPLSM system, carry out two-photon imaging experiments on mouse kidney sections with this system, and verify the ability of the proposed method in fast 3D high-resolution imaging, which is of great significance for the development of MTPLSM.