By using traditional mechanism method to identification is more difficult，a method of the system identification by using BP（Back Proragation）neural network is introduced according to three tanks water control system with traits of time-delay and non-linear. With the parallel connection structure of identification and Levenberg-Marquardt（LM）algorithms or Quasi-Newton algorithms（BFGS） in training network, the simulation shows that the effect of identification is well by using these two kinds of algorithms in BP neural network.