Because the conversion efficiency of thermoelectric (TE) is still an issue, the performance of a three-dimensional helical thermoelectric generation (TEG) system is examined by exposing it to a temperature difference with hot and cold sources. The helical paths for the two thermal fluids give the TEG device the potential to efficiently convert thermal energy. The characteristic performances of the helical system are numerically analyzed by using the finite-volume method in a compact system. The helical system is compared with a straight system in which all the TE elements are established to have an equivalent geometry. The difference between the TE performances of the two systems is not significant when the TE surfaces are maintained at constant temperatures. Therefore, the helical system is a reasonable and feasible design because of its merits, such as compactness and larger and homogenous temperature difference. Both the electromotive force and the current in the TEG system increase linearly with a temperature difference T applied at the two module surfaces. However, the TE performance is affected by the geometry of the helical system. The current preferentially flows through a mainstream path determined by the geometry of the TE element.