A decoupling method for non-linear dynamic system is applied in the familiar non-linear coupled three-tank water system.(Its advantage is that absolute decoupling for the nominal responses of system outputs can be implemented for this kind of system which takes a non-linear compensation way.) The PID control based on BPNN is taken in to this system and simulated in MATLAB. The result proves the efficiency of decoupling method，and shows this system has stronger anti-disturbance characteristic under the control of PID based on BPNN than that of Digital PID.