Belonging to the technical field of air conditioner control, the invention discloses an internal model decoupling control method and control system of a variable air volume air conditioner. The methodincludes: building a three-input three-output model adopting air volume, cold supply water flow and fan rotating speed as the input variables and taking room temperature, supply air temperature and static pressure as the output variables; constructing an internal model control structure; and constructing a decoupling network model, which adopts a multiple-input multiple-output internal model decoupling control method for decoupling, and realizes single-input single-output control of the air volume-room temperature, chilled water flow-supply air temperature and draught fan rotating speed-static pressure. According to the invention, internal model decoupling control is adopted to weaken the coupling performance of the control loop with strong coupling performance, namely the air volume-roomtemperature, chilled water temperature-supply air temperature and fan rotating speed-static pressure, to negligible, and when any control variable changes, the influence caused by the coupling loop can be negligible, and the overall stability and robustness of the variable-air volume air conditioning system are improved.