Pre-stall disturbances and rotating instability (RI) are two typical phenomena observed in axial compressors prior to stall. In this study, experimental measurements and numerical simulations were employed to investigate the relationship between pre-stall disturbances and RI and their physical mechanisms in an axial compressor rotor with a non-uniform tip clearance gap. A post phase-locking technique was used in analyses of pressure fluctuations in the blade tip region. The resulting power spectrum estimation indicated that pre-stall disturbances shared the same frequency characteristics as RI, but differed in their spatial distribution. Pre-stall disturbances were the result of the upstream migration of RI. Numerical simulation results, validated by experimental measured distribution of pressure fluctuations, showed that the tip leakage vortex originating from the large blade tip clearance underwent a spiral-type breakdown, which was the originating mechanism of RI. When the back flow vortex generated by breakdown encountered the blade leading edge due to throttling, pre-stall disturbances were detected at the blade leading edge.