A Tree-based 3D Multilevel FPGA architecture that unifies two unidirectional programmable interconnection network is presented in this paper. In a Tree-based FPGA architecture, the interconnects are arranged in a multilevel network with the switch blocks placed at different tree levels using Butterfly-Fat-Tree network topology. Two dimensional layout development of a Tree-based multilevel interconnect is a major challenge for Tree-based FPGA. A 3D interconnect network technology leverage on Through Silicon Via (TSVs) to re-distribute the Tree interconnects, based on network delay and thermal considerations into multiple silicon layers is discussed. The impact of of Through Silicon Vias and performance improvement of 3D Tree-based FPGA are analyzed. We present an optimized physical design technology leverage on TSV, Thermal-TSV (TTSV), and thermal analysis. Compared to 3D Mesh-based FPGA, the 3D Tree-based FPGA design reduces the number of TSVs by 29% and leads to a performance improvement of 53% based on our place and route experiments.