This paper deals with the study of fractional order system tuning method based on Factional Order Proportional Integral Derivative( FOPID) controller in allusion to the nonlinear characteristics and fractional order mathematical model of bioengineering systems. The main contents include the design of FOPID controller and the simulation for bioengineering systems. The simulation results show that the tuning method of fractional order system based on the FOPID controller outperforms the fractional order system based on Fractional Order Proportional Integral( FOPI) controller. As it can enhance control character and improve the robustness of the system. This paper deals with the study of fractional order system tuning method based on Factional Order Proportional Integral Derivative (FOPID) controller in allusion to the nonlinear characteristics and fractional order mathematical model of bioengineering systems. The main contents include the design of FOPID controller and the simulation for bioengineering systems. The simulation results show that the tuning method of fractional order system based on the FOPID controller outperforms the fractional order system based on Fractional Order Proportional Integral (FOPI) controller. As it can enhance control character and improve the robustness of the system .