Abstract: The current cognitive radio (CR) engine based on genetic algorithm usually adopts a weight-method to change multi-objective into a single objective, which may miss optimal solutions and reduce the efficiency of engine. This paper proposes an adaptive multi-objective immune genetic algorithm with vaccine injection (VAMIGA) to resolve this problem. The vaccine injection could optimize the decision result and convergence speed by saving and recycling the excellent genes. Compared with the strength Pareto evolutionary algorithm (SPEA2) on CR problems, the simulation results show that the VAMIGA reduces 2%~15% of the transmitted power and 6%~36% of the bit error rate (BER), and improves 6%~8% of modulation index. Thus, the VAMIGA can work more efficiently to solve multi-objective optimization and CR waveform design in different environment.