The goal of the current paper is to investigate inner flow behavior on stall inception in a transonic compressor rotor. The stall inception process is numerically carried out by unste- ady 3-D simulations based on the throttle model. The current study shows that stall starts from the tip of the blade, and stall cell extends to the axial, circumferential and radial directions. Through the comparison of flow transition characteristics at different flow rate conditions, the interface between the incoming flow and tip clearance flow shifts forward to the upstream as the mass flow decreases. Eventually, the shock detaches from the blade leading edge, and tip clearance flow spills into the adjacent blade passage, thus stall happens in the affected blade passages.