This paper presents an optimal control method for the prediction of parallel centrifugal variable frequency pump performance in any conditions to maximize the total efficiency of the pump system, thereby minimizing energy consumption. First, a theoretical model of parallel water pumping set was established, after which the shaft power model was setup specifically for the off-rating conditions. By combining the typical polynomial fitting method of the efficiency and the shaft power model we brought up, a new optimized control method was proposed. Using this method, the complex optimization task was solved with the optimal control of the operating number selection and speed ratios for parallel variable speed pumps based on the decision-making. The proposed method was subsequently applied to the pumping set of the water-cooling system in High Magnetic Field Facility. The practical testing results of the proposed method showed its superiority over both the primitive and the previous optimal methods, by considerably lowering the power consumption and accurately calculating the performance parameters in any conditions. The method has universality and simplicity for online implementation, which provides a reference for the control methods of parallel centrifugal pumps in variable flow systems with a differential pressure control strategy.