Using FPGA for general-purpose computing has become an important research direction in high performance computing technology. However, it is not a lossless optimization method. Due to the impact of hardware reconfiguration overhead, data transmission cost, specific characteristics of programs, and other factors, the speedup of general-purpose computing on FPGA has visible difference. On the basis of in-depth analysis of FPGA architecture and development process, the main factors affecting FPGA implementation performance are pointed out, and a parallel cost model for FPGA based on static program analysis is proposed to provide judgment basis for using FPGA in general-purpose computing. The experiment results show that the algorithm estimates accurately FPGA execution performance.