For the under-sampled imaging infrared search and tracking system which Fλ/d<2, the energy of point target was concentrated on a single pixel. Due to the spatial non-uniformity of intra-pixel sensitivity (IPS) for focal plane array, the calculation accuracy of energy and centroid for point target would be reduced. Light spot scanning test and numerical simulation could effectively characterize and analyze the IPS, but the system and model were highly complex and time-consuming, moreover, experimental tests couldn’t analyze the relationship between the spatial non-uniformity of the IPS and the parameters of photo-detector. Aimed at the above problem, Monte Carlo methods were used to simulate the IPS of HgCdTe infrared focal plane array, and the influencing factors of its spatial non-uniformity were analyzed. The results showed that the spatial non-uniformity of IPS can be reduced by reducing the pixel pitch or increasing the thickness of absorber. With the increase in wavelength, the spatial non-uniformity of IPS increased slightly. The results of simulation and analysis are of great significance for improving the measurement accuracy of high energy concentration point target.