Irrigation with water containing a variety of microcystins (MCs) may pose potential threat to normal growth of agricultural plants. The mechanism of microcystin-LR (MC-LR) induced phytotoxicity in rice (Oryza sativa L.) at environmental concentrations is still unknown. Rice seedlings were exposed to MC-LR at concentrations of 0.10, 1.0, 10.0 and 50.0 μg·L−1 in hydroponic nutrient solutions for 7, 15, 20, and 34 days in the current study. The absorption and accumulation in leaf and root tissues, as well as a series of key physio-biochemical process changes in leaves of rice at different exposure time points were measured. Results showed that MC-LR could be detected in rice leaves and roots in all exposure groups, however, a significant accumulation trend of MC-LR in plants (BCF > 1) was only found in the lowest group (0.10 μg·L−1). The time-course study revealed a biphasic response of O2•- levels in rice leaves to the exposure of MC-LR, which was more pronounced in higher concentration groups, which could be attributed to the combined effects of antioxidant and detoxification mechanisms in rice. Exposure to 1.0 - 50.0 μg·L−1 MC-LR resulted in significant depletion of GSH and MDA contents in rice leaves at later exposure times. The changes of nitric oxide synthase (NOS) in rice leaves under MC-LR exposure were firstly investigated in the current study. Low MC-LR concentrations promoted NOS activity, whereas high concentrations inhibited NOS activity during the later exposure times, implying that NO may play a role in MC-LR toxicity in rice. Reduced sucrose synthase (SS) activities in rice exposed to MC-LR can reduce the plant's ability to accumulate carbon and thus may be directly related to the reduction in vegetative growth. These findings suggest that even at low concentrations of MC-LR, terrestrial plants' normal physiological status is disrupted, which, when combined with previous findings, helps reveal the mechanism of MC-LR-induced phytotoxicity.