The growth and physiology of bloom-forming cyanobacterium Microcystis aeruginosa were determined by the flow cytometry when exposed to rice straw extract for 15 d. The cell growth, cell integrity, mitochondrial transmembrane potential, and esterase activity were used to evaluate the physiological response in Microcystis aeruginosa. Rice straw extract stored for 5 days significantly inhibited the growth of Microcystis aeruginosa in a concentration-dependent way; Most of the algae cells (> 98%) remained complete membranes in all the concentration treatments; Compared with the control cultures, the rice straw induced both negative and positive effects on the esterase activity for each test within 4 days, while the inhibition exceeded the stimulation effect. After a 7 d exposure, only the inhibition effect was found. Neither the inhibited nor stimulated effects was observed after algae exposure from 10 d to 15 d. Evident changes was found in the membrane potential during 7 d experiment, whereas inhibition effect became weaker after 10 d and 15 d exposure, in consistent with the result of esterase activity. These results confirmed that the rice straw extract might provide both dominant inhibition and relatively weak stimulation effects. After a long time exposure, inhibition effect became limited while stimulation effect disappeared. The action of rice straw may be algistatic (preventing algal growth) but not algicidal (killing algae).