Abstract: The precise measurement of fluorescence lifetime is of great significance in the fluorescence detection and analysis techniques. Aiming at the problem that the nanosecond fluorescence lifetime cannot be measured directly in the flow cytometry system, a fluorescence lifetime characterization method based on the cross correlation algorithm was proposed, which combined the chirp Z transform (modified chirp Z-transform, MCZT) algorithm with the correlation peak interpolation (fine interpolation of correlation peak, FICP) algorithm.The comparison with the standard fast Fourier transformation (FFT) algorithm was conducted, the fluorescence lifetime of mammalian cells was measured, the obtained data was processed, and the performances of MCZT and FICP algorithms were verified. The experimental results show that the algorithm reduces the fence effect caused by FFT calculation effectively, the resolution ability of the cross-correlation function is improved, and the relative error in measuring fluorescence lifetimes was increased by 4.344 3%.