The invention discloses a fast fluorescence lifetime imaging method based on a single photon avalanche diode detector. The method uses a single photon avalanche diode as a detection device, and photonsampling is carried out through a discretization and aliasing multiplexing detection window. Through a Monte Carlo simulation principle, a fluorescence attenuation curve is fit, and the fluorescencelifetime is calculated. Working of the whole circuit is divided into a detection preparation phase, a detection phase and a readout phase. In the detection phase, laser induces fluorescence excitationof a to-be-detected sample, discretization and aliasing-multiplexing window detection is realized through controlling on the working state of the SPAD and gating when gated gating signals control avalanche pulses caused by photons, and detected data are recorded. The discretization and aliasing-multiplexing detection method is used to expand the best detection range of a time detection window method, and the detection errors are reduced. Two counting modules are integrated in each pixel unit, two groups of data can be sampled after single-time fluorescence excitation, and the imaging speed can be effectively improved.