Traditional loss model of linear induction motors usually only considers iron loss and copper loss. However, the neglect of power electronic losses will reduce the accuracy of model calculations. Moreover, in multi-phase motor drive systems, power electronics losses are relatively higher and cannot be omitted. Considering the above problems, loss models of six-phase inverter under various PWM modulation methods were derived. And combined with an improved dynamic end effect loss model of dual three-phase linear induction motor, a system-level loss model is obtained. Furthermore, optimal excitation current can be calculated based on the model using Newton-Raphson method to minimize system loss. Simulation results showed that this strategy can always bring efficiency improvement under all working conditions, especially under certain light load working conditions (0.2 pu, 5 m/s), the loss reductions of both the inverter and the overall system can achieve by 50% approximately.