Because the secondary regulation transmission system has the factors such as deadzone, hysteresis loop, coulomb friction，it is a typical nonlinear system. It is difficult to obtain famous control effect by use of conventional control method. Based on observerbased method, the application of Hamiltonian function method is studied in a secondary regulation rotate speed systems with the state being not completely measurable. The Hamiltonian form of the secondary regulation hydrostatic transmission system was constructed and a robust observerbased controller was designed, and several results on the asymptotic stability and observerbased robust control problems were presented. The observerbased robust controller has been applied to the secondary regulation transmission speed control system, and the performance simulation has been conducted. The simulation results show that the dynamic characteristics of the system have been improved significantly, with strong antiinterference ability and good robustness.