In order to reduce traffic delay, a novel urban trunk road traffic signal coordinated control method was presented. Firstly, a multi-objective immune algorithm based on multi-population was proposed. By this way, it can effectively prevent population retrogression; promote diversity and the whole optimal searching ability of genetic algorithm. Considering the traffic delay of the uplink vehicles and the down vehicles at different times on the trunk road, the objection function for total delay is set up, and the objection function optimization based on multi-population immune algorithm is implemented through adjusting the phase difference at intersections. Finally, compared with the genetic algorithms and the method of fixed phase difference, the simulation results of this novel control method have verified the obvious advantage.