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Due to the ship dynamic positioning control system is a complex nonlinear system, the conventional PID parameters are difficult to achieve the desired control effect, and the immune electromagnetism-like mechanism(IEM) algorithm is proposed for PID controller parameter self-tuning. In view of the weakness that the electromagnetism-like mechanism(EM) algorithm is easy to fall into the local optimum, the immune information processing mechanism is introduced, and the unique concentration selection mechanism is used to preserve the fine and the particles are close to the optimal position by the immune operator. The performance analysis shows that the IEM algorithm has better stability and better convergence in the self-tuning of PID parameters compared to EM and PSO algorithm. Finally, the position and bow of DP four stage sea condition model are simulated. The simulation results show that compared with the conventional PID controller, the PID controller solved by IEM method has faster response, better stability and smaller steady-state error.