The present study concentrates on the effects of header design on flow mal-distribution in a micro-channel (25 channels) heat sink. Experiments have been conducted to investigate the effect of header shape (rectangular and triangular) on flow mal-distribution and the manufacturing tolerances along the channel length and between the channels. Detailed numerical simulations have been performed for different geometric configurations by varying the header shape (rectangular, trapezoidal and triangular), header size and locations of inlet and outlet (I, C, V, Z and U-type) arrangements. Predicted results clearly illustrate that flow separation and recirculation bubbles occurring in the inlet header are primary responsible for the flow mal-distribution between the channels. To quantify the mal-distribution through the channels, the channel-wise 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.