To improve the precision of micro-polarizer array long-wave infrared imaging system, for the incident light’s polarimetric information calculation problem, a polarimetric calibration method is proposed based on error analysis. By determining the relationship between the pixel level response values and the incident light power, the generalized optical transmittance is introduced to derive and achieve the calculation of the extinction ratio and polarization orientation, further obtain the values of elements in the micro-polarizer Mueller matrix independent of large scale equations. A method to compute polarimetric information in one super pixel which contains fixed position blind pixels is proposed, contribute to getting the incident light’s polarimetric information precisely. The experiments show that this calibration method can effectively reduce error interference, and improve the detection accuray of micro-polarizer array long-wave infrared imaging system.