This paper proposed a two-layer misalignment (MA) measurement error calculation model caused by the pattern center shift. It used the multiple-wavelength measurement methodology to verify that the MA measurement error is linearly proportional to the pattern center shift. The film structure was optimized using the finite-difference time-domain methodology to get confident simulation results. Four different types of asymmetric structures were simulated: a sidewall asymmetric (SWA) structure, two-level SWA structure, SWA with rounding corner structure, and three-level SWA structure with rounding corner. All the simulation results showed a linear relationship between the MA value of multiple-wavelength and the value of pattern center shift. Consequently, an MA measurement correction method was proposed based on the linear property between the MA value of multiple-wavelength and the value of pattern center shift. After the correction, the MA measurement error could be reduced to ±0.04nm for a simple SWA structure with 3.0nm pattern center shift in maximum, to ±0.08nm a for two-level SWA structure with 8.6nm pattern center shift in maximum, to ±0.03nm a for SWA structure with rounding corner with 3.0nm pattern center shift in maximum, and to ±0.02nm a for three-level SWA structure with rounding corner with 1.0nm pattern center shift in maximum