A transportation refrigeration system is provided and includes a trailer refrigeration unit (TRU), a battery to provide electricity for the TRU, an electrical system and a controller. The electrical system includes a direct current (DC) bus electrically interposed between the battery and the TRU. The electrical system further includes an inverter and a boost converter disposed on the DC bus. The controller includes a memory unit storing first, second and third efficiency tables for the TRU, the inverter and the boost converter, respectively, and a processor. The processor sets an operational target for the TRU and achieves the operational target by controlling the inverter and the boost converter according to a voltage of the battery, the first, second and third efficiency tables and real-time operating conditions.