Aiming at the homing problem of the missile under strong counterwork during the terminal guidance, a new fusion tracking algorithm for the radar of the Radar/IR dual-mode missile under intermittent-working state was presented. This algorithm decreased the warning probability of the enemy fighter, the intercepting probability of the enemy missile and the probability of radar being locked–on by Electronic Support Measure (ESM) by decreasing the working time of the radar. To improve tracking precision, the IMM algorithm and UKF algorithm were combined and then applied to the fusion tracking of the radar and the infrared. Simulation results show that, compared with the single infrared tracking, the algorithm improves the tracking precision, decreases the working time of the radar and increases the probability of the hit.