Permanent magnet synchronous motors (PMSMs) with nonconcentric magnetic poles (NCMP) structure are widely used as high-precision servo motors. The current subdomain method mainly equates the NCMP to a rectangular magnet to make each subdomain boundaries of magnet parallel when calculating the magnet eddy current loss (ECL), which results in a lower accuracy of the calculation. This article divides the NCMP into nonconcentric region and concentric region along the radial direction. The nonconcentric region is further divided along the circumferential direction, and each divided region has a single thickness. Based on the subdomain method, a novel analytical method of magnet ECL in PMSMs with NCMPs is proposed. Moreover, the three-dimensional distribution coefficient of ECL in the NCMP is derived by the equivalent impedance method. The effects of eddy current reaction and stator slotting are taken into account to improve the calculation accuracy. Then, through theoretical derivation, the relationship between the minimum magnet loss and the pole parameters is obtained, which provides a reference for the design of NCMPs. Finally, the loss separation experiment is performed on four prototypes with NCMPs. The experimental results, finite element method results and analytical results are compared to verify the correctness of the model.