This study addresses the issue of large measurement errors in microarray polarized navigation sensors and conducts research on calibration methods for polarized light navigation sensors. Firstly, the non-uniformity error of the photoelectric pixel response in the microarray polarized navigation sensor and the inconsistent coupling error between the nano-grating array and the photoelectric pixel are analyzed. A measurement error model for the microarray polarized navigation sensor, including irradiance non-uniformity error and coupling inconsistency error, is established. Secondly, a calibration method for irradiance non-uniformity error based on curve fitting is proposed to effectively compensate for errors in the photosensitivity and bias coefficients of the photoelectric pixel. For the coupling inconsistency error between the nano-grating array and the photoelectric pixel, a calibration method based on rotational angle measurement is proposed. Finally, a calibration test platform for the microarray polarized navigation sensor is built. Experimental results after calibration show that the angular measurement accuracy of the microarray polarized navigation sensor is 0.0461° under standard light sources, an improvement of 91.9% compared to the previous results. In outdoor environments, the angular measurement accuracy of the navigation sensor is 0.2404°, an improvement of 40.72% compared to the previous results, providing a foundation for achieving high-precision polarization navigation.