A method for calculating axis deviation of rotor assembly based on end face runout measurement comprises three parts: calculation of three contact points, a triangle judgment criterion and a homogeneous coordinate transformation algorithm of a deviation matrix. Based on the measured end face runout data in production practice, the method realizes the prediction of axis deviation before assembly, improves the concentricity of rotors after assembly, also greatly increases the one-time acceptance rate of assembly and has important practical guiding significance for axis prediction as well as assembly phase adjustment and optimization in the assembly process of aero-engine rotor pieces.