Maintaining the s-polarization state of laser beams is important to achieve high modulation depth in a laser-interference-based super-resolution structured illumination microscope (SR-SIM). However, the imperfect optical components can depolarize the laser beams hence degenerating the modulation depth. Here, we first presented a direct measurement method designed to estimate the modulation depth more precisely by shifting illumination patterns with equal phase steps. This measurement method greatly reduces the dependence of modulation depths on the samples, and then developed a polarization optimization method to achieve high modulation depth at all orientations by actively and quantitatively compensating for the additional phase difference using a combination of waveplate and a liquid crystal variable retarder (LCVR). Experimental results demonstrate that our method can achieve illumination patterns with modulation depth higher than 0.94 at three orientations with only one LCVR voltage, which enables isotropic resolution improvement.