•A new model for automobile exhaust thermoelectric generator system is proposed.•Based on the system reliability, the counter flow cooling pattern is recommended.•There exists an optimal thermoelectric unit number to maximize system output power.•Better performance is predicted with less thermoelectric materials consumption. This work develops a multiphysics thermoelectric generator model for automobile exhaust waste heat recovery, in which the exhaust heat source and water-cooling heat sink are actually modeled. Special emphasis is put on the non-uniformity of temperature difference across thermoelectric units along the streamwise direction, which may affect the performance of exhaust thermoelectric generator systems significantly. The main findings are: (1) The counter flow cooling pattern is recommended, although it cannot elevate the overall output power as compared with the parallel flow counterpart, it reduces the temperature non-uniformity effectively, and hence ensures the system reliability. (2) The temperature non-uniformity strikingly deteriorates the output power of thermoelectric unit along the streamwise direction; meanwhile, an additional lateral heat conduction effect exists within the exhaust channel wall, the both mechanisms leads to that the maximum output power of the system is not enhanced but is actually reduced when too many thermoelectric units are adopted. (3) When the exhaust channel length is fixed, the maximum output power of the system can be elevated by increasing the thermoelectric unit number but keeping thermoelectric unit spacing unchanged. This means that the system performance can be improved under the condition of less thermoelectric materials consumption.