Abstract: HFPGA (hierarchical FPGA) is a common FPGA architecture in industry.An improved partition algorithm is proposed,which based on previous works about hierarchical FPGA partitioning.The algorithm combines the simulated annealing algorithm with ratio-cut method to ascertain the level of the multi-level multi-way partitioning. Considering the number of cut lines while partitions CLB into cluster,it achieves a better partition result and improve the usage in HFPGA,then optimize the FPGA performance.