As a new computing architecture, reconfigurable computing can achieve potentially much higher performance than software, while maintain a higher level of flexibility than hardware, so it has become a hotspot of current computer architecture research field. The main technique basic of reconfigurable computing is Field Programmable Gate Arrays(FPGA) and it's architecture is constitutive of the reconfigurable hardware and Micro-processing unit. One type of the reconfigurable architecture is that the Micro-processor is embedded into the reconfigurable hardware. This paper presents some improvements for FPGAs reconfigurable resource utilization algorithm with Genetic Algorithms. It is found that the new algorithm is more efficient. It can get the tradeoff between the system performance and the reconfigurable resource utilization efficiency.