With the ever-increasing design complexity in the processor micro-architecture, performance analysis becomes more and more important in the research and design of processors. Performance models are used widely in the performance analysis, which are more suitable for the design space exploration in the early stage. When used in microarchitecture optimizations, the accuracy and the speed of performance models are the limiting factors. Therefore, a performance analysis method based on counters was proposed. In this method, the RTL register transfer level code of a processor core was used as a baseline, and a specialized performance monitor unit was added to collect the events needed by the micro-architecture analysis and optimization. Then the collected events were sent to a result analyzer, where the factors affecting the performance were obtained. By a dopting the method, we analyzed what affects the performance in running SPEC CPU2000 benchmarks on FPGA(field-programmable gate array) prototyping, and optimized the micro-architecture of processor core according to the analysis results. The performance of the optimized processor core is improved obviously.