A system and method for configuring a transport refrigeration unit (TRU) battery charger in a transport refrigeration system (TRS) is provided. The method includes receiving battery topology data indicating a battery topology of a TRU battery equipped in the TRS. The method also includes determining specific parameters for configuring a battery charging algorithm based on the battery topology data. Also, the method includes the TRU battery charger configuring the battery charging algorithm based on the specific parameters.