The central shaft is an important and indispensable part of a small scale urban vertical axis wind turbines (VAWTs). Normally, it is often operated at the same angular velocity as the wind turbine. The shedding vortices released by the rotating shaft have a negative effect on the blades passing the wake of the wind shaft. The objective of this study is to explore the influence of the wake of rotating shaft on the performance of the VAWT under different operational and physical parameters. The results show that when the ratio of the shaft diameter to the wind turbine diameter (α) is 9%, the power loss of the wind turbine in one revolution increases from 0% to 25% relative to that of no-shaft wind turbine (this is a numerical experiment for which the shaft of the VAWT is removed in order to study the interactions between the shaft and blade). When the downstream blades pass through the wake of the shaft, the pressure gradient of the suction side and pressure side is changed, and an adverse effect is also exerted on the lift generation in the blades. In addition, α = 5% is a critical value for the rotating shaft wind turbine (the lift-drag ratio trend of the shaft changes differently). In order to figure out the impacts of four factors; namely, tip speed ratios (TSRs), α, turbulence intensity (TI), and the relative surface roughness value (k s /d s ) on the performance of a VAWT system, the Taguchi method is employed in this study. The influence strength order of these factors is featured by TSRs > k s /d s > α > TI. Furthermore, within the range we have analyzed in this study, the optimal power coefficient (C p ) occurred under the condition of TSR = 4, α = 5%, k s /d s = 1 × 10 −2 , and TI = 8%.