Numerical methodology identifying the d-q axis parameters for Interior Buried PM Synchronous Motor (IPMSM) with multi-layered PM has been proposed. In addition, cross-magnetization between d-q axis in IPMSM with the magnetic saturation is investigated via the newly adopted synthetic flux linkage, which can be identified numerically and experimentally. Numerically identified synthetic flux linkages by Finite Element Analysis(FEA) are validated with the experimental ones for the purposely-built prototype, and their further effectiveness on the application is proposed. The design methodology using the proposed synthetic flux linkage for satisfying the design objectives according to operating condition at the same time is proposed. In addition, proposed synthetic d-q flux linkage can be applied to the current reference generation and feed-forward compensation in the current control.