The aerodynamic and flutter effects caused by the circumferential non-uniform tip clearances from the non-axisymmetric casing geometry, which are more representative of real operational conditions, should receive more attention. In this paper, sensitivity analyses on clearance and non-uniformity regarding rotor performance are conducted. The isentropic efficiency, total pressure ratio and stability margin of the rotor are reduced by 1.96%, 1.06% and 6.76% for an increase of tip clearance by 1% tip chord, respectively. The non-axisymmetric configuration reconfigures the interaction between leakage flow and mainstream in each rotor passage and alters the strength and influence range of the low-speed separation region generated by shock wave. The phase lag phenomenon observed in the aerodynamics of the non-axisymmetric layout also manifests in the aeroelastic effects but requires a larger phase shift at the maximum clearance sector, owing to the longer timescales for flow adjustment relative to the local tip gap considering the flow-induced vibration. Clearance sensitivity on flutter stability varies with the direction of the traveling wave: under forward traveling conditions, damping values initially decrease and then increase with increasing rotor tip clearance; while under backward traveling condition, blade damping linearly decreases with increasing rotor tip clearance. Additionally, variations in flow conditions and nodal diameters affect flutter stability by altering the position of shock waves and their work on the suction surface of the rotors. The mechanism responsible for unsteady flows induced by non-axisymmetric clearances from the casing ovalization on flutter stability is discussed for the first time in this paper, which can guide the industry to evaluate its impact.