The transfer matrices method of multibody system is effective methods which solve the dynamics problem of controlled multibody system. The transfer matrices of control actuator element, control feedback element, other elements and overall transfer matrices of the controlled multibody system were developed to deal with the controlled multibody system with branch. The motion of the controlled multibody system with branch was computed by controlled multibody system transfer matrix method and Newton-Euler method. The computation show that the results obtained by controlled multibody system transfer matrix method is effective.