In order to uncover the effects of phosphorus (P) nutrition deficiency on volatile organic compounds (VOCs) released from cyanobacteria and their allelopathic effects on other algae in freshwater bodies, the VOCs from Microcystis aeruginosa that is the main species of cyanobacterial bloom in non-P medium were analyzed, and their effects on Chlamydomonas reinhardtii cell growth, photosynthetic pigment content and photosynthetic abilities were determined in this study. The VOC types and emission amount increased after M. aeruginosa cells were kept in non-P medium for 24 h, with the increase of 73.4% of the total emission amount in contrast to that in normal medium. Meanwhile, 7 new compounds appeared. There was no significant difference in C. reinhardtii growth after the algal cells were exposed to the VOCs from M. aeruginosa in normal medium. However, C. reinhardtii growth was markedly inhibited by the VOCs from M. aeruginosa in non-P medium, with the response index (RI) of -0.25. Meanwhile, the photosynthetic pigment content, maximum quantum yield of photosystem Ⅱ (PSⅡ) photochemistry (Fv/Fm), effective quantum yield in PSⅡ photochemistry, coefficient of photochemical quenching (qP) and apparent electron transport rate through PSⅡ (ETR) in C. reinhardtii also reduced remarkably, while non-photochemical dissipation of absorbed light energy (NPQ) increased significantly, with the RI of 0.26. Therefore, P deficiency caused by cyanobacteria mass propagation and P sedimentation in eutrophicated water might induce cyanobacteria releasing abundance of VOCs, which might play allelopathic inhibitory roles in cyanobacteria keeping advantages for nutrition competition and the reduction of algal biodiversity in water bodies.