We report a generally designed optical modulation method to garner the tunable three-dimensional (3D) polarized optical multi-focal spots arrays in the focusing system of high numerical aperture (NA) objective lens, and it has good compatibility with vector beams of different polarization states. Based on the vector angular spectrum theory and Fourier transform, the vector light fields of Gaussian beam, Bessel-Gaussian (BG) beam and Laguerre-Gaussian (LG) beam are modulated with the generally designed multi-focal spots phase filter (MSPF). Meanwhile, a generally designed sidelobe suppression transmission (SST) function is employed to reduce the interference effect of the adjacent focal spots in the arrays. Thus, the one-dimensional (1D) axial multi-focal spots array and the 3D multi-focal spots arrays with high spatial resolution can be generated. The MSPF is flexible and reliable in modulating various vector beams, and exhibiting high tunability for the number (3, 12, 21), spacing (4λ—11.3λ) and spatial distribution (1D—3D) of focal spots in the array. With the generally designed MSPF, the generation of multi-focus array is promoted to be more universal and flexible and shows potential application prospects in femtosecond laser multi-beam parallel processing, particle capture, as well as high-density data storage.