Optical system for measuring the fluorescence lifetime is built up according to the principle of time correlation single photon counting, and the characteristics of single photon emission of single quantum dots are verified experimentally. The fluorescence lifetime of quantum dots with single photon emission properties on different substrates of quartz glass slide, silicon wafer and gold film is measured and compared for different effective distances between quantum dots and substrates. The experimental results are explained with theoretical simulation results of correlation of fluorescence decay rate and quantum yield with effective distance. The blinking properties of single quantum dots on different substrates are recorded and analyzed. The experimental results show that different substrates can effectively modify the fluorescence blinking and fluorescence decay rate of single photon emission of single quantum dots.