In this article, the effects of clocking effect on performance and vibration intensity of a five-stage centrifugal pump were investigated by experimental tests. The vibration characteristics of five positions in the pump were measured, including axial direction of the pump and horizontal and vertical directions of pump inlet and outlet. There are eight clocking schemes between the impellers in the test, which are arranged by orthogonal experimental design. The test results show that the clocking effect of impellers has little effect on the head and efficiency of the five-stage pump in the whole flow rate. Compared with the results of 0°stagger angle clocking scheme between each impeller, in the whole flow rate, the pulsation of pump head and efficiency is just 1.5% and 1.3%, respectively, under other clocking schemes of impellers. Instead, the impeller clocking has a significant effect on the vibration characteristics of the model pump. The maximum vibration intensity of the five-stage pump locates in the vertical direction of pump inlet within the whole flow rate. Under the best clocking scheme of impellers, the maximum vibration intensity of the pump can decrease by 23.1% and the mean vibration intensity can decrease by 17.3%.