In this research, a structure modification based PID neural network (PIDNN) decoupling strategy is proposed to solve the difficulty in controller caused by the strong coupling in nonlinear multivariable systems. Incomplete differential neurons are first introduced into the hidden layer of the PIDNN, which achieving a decreased amount of control overshoot and better control stability. Then, an improved integration strategy is incorporated in the hidden layer structure, resulting in expedited convergence speed in the PIDNN control. Furthermore, intelligent optimization algorithms are employed to improve the convergence rate of the proposed PIDNN. The stability of the proposed controller is analyzed, and an adaptive learning rate scheme is derived. Finally, to confirm the effectiveness of the controller, three examples and the analysis of experimental results are provided.