—Multi-mover motors are widely used in logistics transportation systems. However, the unique number of movers and variations in motion states complicate the distribution of loss and thermal characteristics, thereby increasing the difficulty of calculating temperature rise. In this paper, a winding loss calculation method that considers the multi-condition and dynamic characteristics of multi-mover motors is proposed. The convective heat transfer coefficient (CHTC) is calculated using computational fluid dynamics (CFD) and response surface methodology (RSM), with a detailed analysis of velocity distribution characteristics. The interactive effects of mover speed, acceleration, mover quantity, and the distance between adjacent movers on the CHTC are investigated. A simplified yet accurate thermal modeling is developed, reducing the required time for a single operating condition from 4 h to 0.5 h, with an error of only 4 %. Through both single variable and multivariable analyses, the thermal characteristics of multi-mover motors under different conditions are revealed. Finally, a prototype is created and tested under various operating conditions. The discrepancies between the experimental and calculated values are within 5 %, validating the accuracy of the proposed model and analysis.