Thermoelectric (TE) performance of a three-dimensional (3-D) TE module is examined by exposing it between a pair of counter-flows of ideal fluids. The ideal fluids are thermal sources of TE module flow in the opposite direction at the same flow rate and generate temperature differences on the hot and cold surfaces due to their different temperatures at the channel inlet. TE performance caused by different inlet temperatures of thermal fluids are numerically analyzed by using the finite-volume method on 3-D meshed physical models and then compared with those using a constant boundary temperature. The results show that voltage and current of the TE module increase gradually from a beginning moment to a steady flow and reach a stable value. The stable values increase with inlet temperature of the hot fluid when the inlet temperature of cold fluid is fixed. However, the time to get to the stable values is almost consistent for all the temperature differences. Moreover, the trend of TE performance using a fluid flow boundary is similar to that of using a constant boundary temperature. Furthermore, 3-D contours of fluid pressure, temperature, enthalpy, electromotive force, current density and heat flux are exhibited in order to clarify the influence of counter-flows of ideal fluids on TE generation. The current density and heat flux homogeneously distribute on an entire TE module, thus indicating that the counter-flows of thermal fluids have high potential to bring about fine performance for TE modules.