Fluorescence lifetime imaging microscopy is a widely used technique in microscopy imaging. In this paper we introduced cross-correlation phase counting method for digital frequency domain Fluorescence lifetime imaging microscopy and revised some mathematical modeling based on it. To verify the result of revised model, we firstly used Matlab to simulate this process and compared the results between four and eight sampling windows. And then we implemented both four and eight sample window system on FPGA, which exhibits that eight sample window performs better than four sample window.