Microcystins (MCs) and other toxic metabolites, released from cyanobacterial blooms, can be transferred to farmland via irrigation and therefore may have adverse effects on terrestrial crops. In the present study, the net photosynthetic rate, transpiration rate, stomatal conductivity and chlorophyll fluorescence, as well as the ultrastructural features of leaves of rice (Oryza sativa L.) at vegetative stage were investigated under the exposure to a series of concentrations of MC-LR (0.1, 1.0, 10.0, 100.0 and 500.0μg/L) and Microcystis aeruginosa crude extracts (0.002 lysate, 0.02 lysate and 0.2 lysate) for 21days. Results showed that exposure to pure MC-LR can produce significant inhibitory effects on the photosynthetic characteristic parameters of rice, and the transpiration rate and stomatal conductivity are the most sensitive indicators in rice to MC-LR exposure. In contrast, different effect characteristics of photosynthesis parameters, even the stimulating and promoting effects, were found in rice under the exposure to Microcystis aeruginosa crude extracts (e.g. significant induction of the transpiration rate and stomatal conductivity of rice under the exposure to 0.02lysate). In addition, a series of ultrastructural alterations were also found in rice leaves exposed to high levels of the pure MC-LR and Microcystis aeruginosa crude extract. These results suggested that the toxicity mechanism of Microcystis aeruginosa crude extracts to rice is different from pure MC-LR and the decrease of biological toxicity might be due to the changes of MCs bio-availability caused by the interactions with other components co-existed in crude extract solution.