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The wheel-based humanoid robots with waist mechanism have large workspace and high agility. The humanoid robot in this paper has a waist mechanism with two parallel driving motors. The waist mechanism connects the vehicle with the trunk of the humanoid robot. The dynamic characteristic of the waist mechanism is affected by the dynamic characteristic of arms and vehicle and the external forces or torques, as well as by the motion of its own. This paper firstly built the whole dynamic model of the humanoid robot using the effective Newton-Euler Algorithm and then built the dynamic model of the waist mechanism through simplifying the whole dynamic model without consideration of coupling motion of the joints. The simplified dynamic model expresses the dynamic relation among the vehicle, waist and arms of the humanoid robot, minimizes the calculation and is convenient for realizing the control algorithm based on the dynamic model. This paper presented the PD control and the calculated torques method for compensating the torque disturb as the control strategy of the waist mechanism based on its dynamic model. The simulation shows the control algorithm remarkably improves the position tracing precision of the waist mechanism and improves the work precision of the humanoid robot.