Based on an analysis of imaging process of 288×4 FPA (Focal Plane Array) thermal imaging system with vertical micro-scanning, a processing algorithm for realizing sub-pixel imaging was proposed. The method doubles the cut-off frequency in vertical MTF (Modulate Transfer Function) of the detector, and markedly improves the system imaging quality and action range. The algorithm is simple, the amount of treatment is small, and a real time processing is easily achieved. The realization of this algorithm has great significance in improving technological tactic performance of thermal imaging systems.