Disclosed are a method and system for measuring concentricity and the tip clearance of a rotor and a stator of an aero-engine. The method comprises the steps that the clearance amount of the rotor and the stator of the aero-engine at an initial measurement point is acquired; a clearance maximum jerk value FIR value, the phase of the clearance maximum jerk value FIR value, a maximum deviation IMP value between a sampling profile curve concave point and a mean profile, the phase of the maximum deviation IMP value, an eccentric distance ECC value, the phase of the eccentric distance ECC value, a maximum clearance value relative to the rotation center, the phase of the maximum clearance value, a minimum clearance value relative to the rotation center, the phase of the minimum clearance value, a maximum clearance value relative to the geometric center, the phase of the maximum clearance value, a minimum clearance value relative to the geometric center and the phase of the minimum clearance value are obtained; an angle-clearance distribution diagram is drawn; the clearance amount is corrected in the horizontal placement measurement process; a concentricity error value and the tip clearance of the rotor and the stator of the aero-engine are obtained. The system comprises a sampled data analysis module, a rotor and stator concentricity calculation module, a tip clearance analysis and calculation module and a horizontal-measurement deflection correction module. The method and system are suitable for measuring the concentricity and the tip clearance of the rotor and the stator of the aero-engine.