Allelopathic interactions among phytoplankton species are regarded as one of the important factors contributing to their dominance and succession in natural waters. Microcystis aeruginosa is a cyanobacterial species commonly found in eutrophic lakes, and microcystin-LR (MC-LR), the mainly secondary metabolite in its cells is usually regarded as allelochemical. However, the biological role of this molecule in the aquatic ecosystem is still under discussion. To explore and distinguish the allelopathic effects of MC-LR and other secondary metabolites on phytoplankton, the dose-effects relationships between MC-LR and growth as well as effective quantum yield of Chlorella vulgaris were investigated. In addition, the different responses of C. vulgaris exposed to pure MC-LR (200 μg/L) that has been proved to induce negative effects, the cell-free filtrates and crude extracts of toxic M. aeruginosa FACHB-905 in cell concentration containing the same content of MC-LR were compared. The results showed that MC-LR decreased the growth and effective quantum yield of C. vulgaris, and the inhibition efficiency increased with enhanced MC-LR concentration. Contamination with MC-LR ≥ 200 μg/L significantly inhibited the growth and effective quantum yield of C. vulgaris in concentration of 1500 μg/L chlorophyll-a within 24 h. The cell-free filtrates of toxic M. aeruginosa FACHB-905 had no significant negative effects on C. vulgaris. However, compared with the pure MC-LR, the crude extracts of toxic M. aeruginosa FACHB-905 containing the same amount of MC-LR led to further inhibition. Compared with the MC-LR treated one, the growth and effective quantum yield of C. vulgaris treated with the crude extracts was further decreased by 14% and 3%, respectively. The results indicated that the allelopathic effects of MC-LR on its co-existing phytoplankton species were dose-dependent, and the secondary metabolites other than MC-LR also had negative effects.