The invention discloses a coordination control method for the trajectory of a two-freedom-degree joint robot. According to the control method, Hamiltonian with an end port controlled is combined with PD control; an exponential function is adopted as a coordination control function of the Hamiltonian with the end port controlled and PD control; by adjusting the control degrees of two control methods, the action degree of PD control is large at first, and the system is made to have good fast tracking performance; and control of the Hamiltonian with the end port controlled is large in action degree during the steady state, and the system is made to have good steady state performance. By means of the method, the dynamic response performance of a whole robot movement system is improved, the system can fast enter steady state running, the rising time and the adjusting time of the system are shortened, and the control precision of the system is also improved. Due to the coordination control scheme, the advantages of each control method are utilized most efficiently during the corresponding time period, and therefore high application value is achieved.