Haematococcus pluvialis is one type of freshwater unicellular microalgae, belonging to the Chlorophyta, Haematococcus.H. pluvialis has high economic value due to its wide variety of nutritional components, including astaxanthin, vitamins, algal polysaccharides, proteins, etc. Current microalgae detection methods are deficient in monitoring the life cycle of H. pluvialis. In this study, we applied the confocal fluorescence microscopy and the fluorescence lifetime imaging microscopy (FLIM) system to observe the different stages of the microalgal cells. The cell morphology and the fluorescence lifetime distributions were obtained for further analysis. The results showed that H. pluvialis had a diameter of about 25 μm in the state of flagellated macrozooids (zoospore). When the nutrients in the medium were continuously consumed, the individual cells of H. pluvialis became larger and entered the microzooid stage, whose diameters were around 35 μm. The fluorescence lifetime values of H. pluvialis in the macrozooid (zoospore) stage and the microzooid stage were around 700-800 ps and 1000 ps, respectively. The next stage was the palmella stage, in which the diameter of H. pluvialis increased to the range of 40-52 μm. During this stage, the larger algae began to accumulate red pigment in the center of the cell.Meanwhile, the fluorescence lifetime values near the center of the algal cell increased to around 1300 ps, approximately 200 ps higher than the values in the periphery of the cells, showing layered properties of H. pluvialis in the palmella stage.In summary, FLIM can provide a real-time quantitative method for monitoring different life stages and cell morphologies of H. pluvialis during its life cycle in a non-destructive way.