To explore the factors affecting the temperature of the three dimensional Field Programmable Gate Array(FPGA) chip，a finite element simulation model targeted three dimensional FPGA is proposed. First，the model is constructed using commercial software Flotherm based on Through Silicon Via(TSV)，micro bump，flip chip eutectic bump，interposer，Ball Grid Array(BGA) solder ball and PCB. Then，the model is adopted to analyze the temperature of the three dimensional FPGA chip with different numbers of TSVs and stacking layers from qualitative and quantitative point of view. It is found that the average temperature increases from the bottom chip to the top chip，and the average temperature of each layer increases with the decrease of the number of TSVs and the increase of the number of stacking layers. The experimental results are consistent with the results published in the literature, indicating the feasibility of the proposed simulation model in the analysis of the parameters influencing the temperature of the chip.