For the entry vehicle equipped with RCS (reaction control system) and rudder, an optimal control allocation method based on PWPF (pulsewidth pulse-frequency) modulator was proposed. By transforming the discrete control signal of RCS into the continuous quantity, the control allocation problem was constructed as a quadratic programming problem. And the active-set method was used to solve the quadratic programming problem. Then, the on-off signal of RCS was obtained by using the discrete method and PWPF modulator. Compared with the mixed integer programming problem, the quadratic programming problem is easier to be solved, which is favorable for on-board computing. The proposed method has the fault-tolerant ability by reconstituting the quadratic programming problem.