The invention provides a control method and system of a water chilling unit. The control method of the water chilling unit comprises the steps that evaporator pressure and condenser pressure of the water chilling unit are detected; a target value of the intermediate pressure is obtained according to the evaporator pressure and the condenser pressure, wherein the intermediate pressure indicates pressure between a primary throttling device and a secondary throttling device of the water chilling unit; and the opening degree of the secondary throttling device is adjusted according to the target value of the intermediate pressure. By means of the control method of the water chilling unit, the operational frequency range of the water chilling unit can be effectively expanded, and the operating efficiency of the water chilling unit under part of operating loads is improved.