The frequency-agile radar performs well in electronic countermeasures, making up for the shortage of traditional radar. It has many advantages and has been widely applied. The carrier frequency variation of agile radar cannot lead to coherent processing like traditional methods, which makes many phase information incapable of being used and reduces radar detection performance. In this paper, Agility coherent signal model is established and its signal characteristics are analyzed. Different from the traditional radar signal processing methods, the coherent processing of Agility coherent signal is established. The influence factors of the velocity side lobe of the agility coherent radar are obtained according to the coherent processing. By analyzing the relevant factors, an intelligent algorithm, namely simulated annealing algorithm (SAA) is used to optimize the side lobe suppression. Inspired by mismatched filter, we design corresponding velocity dimensional mismatch filter and carry out experimental simulation. Simulation results show that the method is effective.