Recent years has witnessed miniaturization, integrity and modularization of electronic products, leading to the escalation in terms of assembly density of electronic components and decrease in terms of effective thermal dissipation area. Therefore, thermal design of high-power electronic components and thermal dissipation problems at board level become so prevalent among electronic engineers. For FPGA (field programmable gate array) system, thermal dissipation is one of the pivotal technologies determining whether the chip is capable of normally working. The purpose of PCB thermal design is to decrease the temperature of components and the board through suitable measures and methods in order to make system work under suitable temperature. In spite of numerous measures to dissipate heat of PCBs, some requirements must be taken into account such as thermal dissipation cost and practicability. This article comes up with thermal design methods for PCBs controlled by FPGA system based on the analysis of the practical thermal dissipation problems to ensure the excellent thermal dissipation capability of FPGA system control board.