In the infrared focal plane array (IRFPA) imaging system, the non-uniformity (NU) of IRFPA directly affects the quality of infrared images. Especially applying in the infrared weak small targets detection and tracking system, the impact of the spatial noise caused by the non-uniformity of IRFPA detector, often more serious than the temporal noise of imaging system. In order to effectively correct the non-uniformity of IRFPA detector, we firstly analyze main factors that cause the non-uniformity of IRFPA detector in imaging. Secondly, according to photoelectric conversion mechanism of IRFPA detector, and the analysis of the process of the target energy accumulation and transfer, we propose a calculation method of pixels' integral capacitance. Then according to the calculation results, we correct the original IR image preliminary. Finally, we validate this non-uniformity correction algorithm by processing IR images collected from actual IRFPA imaging system. Results show that the algorithm can effectively restrain the non-uniformity caused by the differences of the pixels' capacitance.