Abstract: In order to explore the effect of chlorophyll on the proliferation of specific intestinal bacteria at the bacterial species level, this study firstly explored the feasibility of flow cytometry (FCM) to count intestinal bacteria and compared it with the dilution plating method. Then, the effects of chlorophyll on the proliferation of Flavonifractor plautii, Bacteroides vulgatus, Bifidobacterium pseudolongum and Lactobacillus murinus were investigated by FCM. The results showed that FCM could detect live bacteria and dead bacteria at the same time. There was a good correlation between the count of live bacteria by FCM and the number of live bacteria determined by the dilution coating method (r>0.8, P<0.001). However, detection efficiency of FCM was higher, and the detection results were closer to the real value. 100 µg/mL chlorophyll highly significantly promoted the proliferation of Flavonifractor plautii (P<0.01), while 300 and 500 µg/mL chlorophyll extremely significantly inhibited the proliferation of Flavonifractor plautii (P<0.001). 100 µg/mL chlorophyll extremely significantly promoted the proliferation of Bacteroides vulgatus (P<0.001), while 300 and 500 µg/mL chlorophyll extremely significantly inhibited the proliferation of Bacteroides vulgatus (P<0.001). Chlorophyll could extremely significantly inhibit the proliferation of Bifidobacterium pseudolongum (P<0.001), and the higher the concentration was, the stronger the inhibitory effect was. Chlorophyll could extremely significantly promote the proliferation of Lactobacillus murinus (P<0.001), and the higher the concentration was, the stronger the promoting effect was. This study would provide important theoretical data for elucidating the effect of dietary chlorophyll on the growth of gut microbiota.