How to design silicon-based quantum wires with a figure of merit (ZT) larger than three is under hot pursuit due to the advantage of low cost and the availability of matured fabrication techniques. Quantum wires consisting of finite three-dimensional quantum dot (QD) arrays (QDAs) coupled to electrodes are proposed to realize high efficient thermoelectric devices with optimized power factors. The transmission coefficient of 3D QDAs can exhibit 3D, 2D, 1D and 0D topological distribution functions by tailoring the interdot coupling strengths. Such topological effects on the thermoelectric properties are revealed. The 1D topological distribution function shows the maximum power factor and the best ZT value. We have demonstrated that 3D silicon QDA nanowires with diameters below 20 nm and length 250 nm show high potential to achieve ZT ≥ 3 near room temperature.