To ensure the variable diffuser vane can rotate around a pivot fluently in practical applications, there have to be clearances between vanes and diffuser walls. As the compressor pressure ratio increases, the effects of the vane endwall clearances are enhanced and cannot be ignored. This paper investigates the effects of both-side vane endwall clearances on the centrifugal compressor performance. Results show that the existence of endwall clearances mainly enlarges the flow capacity of the vane diffuser and decreases the compressor efficiency, and these effects are more significant as the vane stagger angle decreases. A one-side endwall clearance of 2.7% of the diffuser width increases the choke mass flow rate by as much as 20% and decreases the compressor peak efficiency by 2.7%. Due to the non-uniform flow along span at the impeller outlet, the shroud-side vane endwall leakage plays a more important role than the hub-side in affecting the compressor performance. In additions, the respective contributions of the vane throat, the hub-side and the shroud-side endwall clearances to the increases of the vane choke mass flow rate are quantitatively studied. The flow physics and loss mechanisms of the endwall leakage are revealed.