Thermoelectric (TE) performance of a three-dimensional (3D) TE module is examined by exposing it between a pair of counter-flows of ideal fluids. The ideal fluids as thermal sources of TE module flow in the opposite direction at same flow rate and generate temperature difference on the hot and cold surfaces due to their different temperature at channel inlet. TE performance caused by different inlet temperature of thermal fluids are numerically analyzed by using finite-volume method on 3D meshed physical models and then compared with those of using constant boundary temperature. The results show that voltage and current of 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 hot fluid when inlet temperature of cold fluid is fixed. However, the time to get the stable values is almost consistent for all the temperature differences. Moreover, the trend of TE performance using fluid flow boundary is similar to that of using constant boundary temperature. Further, 3D 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 entire TE module, thus indicating that the counter-flows of thermal fluids have high potential to bring fine performance for TE module.