The circumferential and axial widths of permanent magnet (PM) pole and E-shape stator pole of linear rotary motor with interlaced PM poles are very influential to the back electromotive force (EMF) and the flux leakage analysis is complex, which causes difficulty in optimization of the motor structure. One of the key issues in optimization design is to calculate the flux leakage accurately. In this article, the main flux and side flux variation laws of stator pole are derived by analytical method. The flux leakage can be divided into the flux leakage between the PM and the mover, flux leakage on the stator tooth tip, and the flux leakage between the adjacent PM poles and stator pole. The 3-D flux leakage calculation model is built, which is suitable for the calculation of magnetic flux based on different motor operating principles. Then the rotational and rectilinear back EMFs are calculated by analytical method, which are consistent with the results analyzed by 3-D finite element method.