The optical joint transform correlator (JTC) has been used in target real-time recognition, but the anti-distortion performance has always been the difficult problem for recognition system, which limits its further development and application. In this paper the principle and experimental system of JTC are introduced. The effect of target distortion is analyzed and the optimization method is proposed. The synthetic discriminate function and the power subtraction are applied to process the joint power spectrum and eliminate zero-order correlation peak. The result shows that the optimization methods can enhance the output peaks and improve the anti-distortion performance of joint transform correlator for target identification.