Microcystis is a notorious cyanobacterial genus due to its rapid growth rate, huge biomass, and producing toxins in some eutrophic freshwater environments. To reveal the regulatory factors of interspecific competition between toxic and non-toxic Microcystis, three dominant Microcystis strains were selected, and their photosynthesis, population dynamics and microcystins (MCYST) production were measured. The results suggested that nitrogen-limitation (N-limitation) had a greater restriction for the growth of toxic Microcystis than that of non-toxic Microcystis, especially when cultured at high light or high temperature based on the weight analysis of key factors. Comparison of photosynthesis showed that low light or N-rich would favor the competitive advantage of toxic Microcystis while high light combined with N-limitation would promote the competitive advantage of non-toxic Microcystis, and these two competitive advantages could be further amplified by temperature increase. Mixed competitive experiments of toxic and non-toxic Microcystis were conducted, and the results of absorption spectrum (A(485)/A(665)) and qPCR (real-time quantitative PCR) suggested that the proportion of toxic Microcystis and the half-time of succession process were significantly reduced by 69.4% and 28.4% (p < 0.01) respectively by combining N-limitation with high light intensity than that measured under N-limitation condition. N-limitation led to a significant decrease of MCYST cellular quota in Microcystis biomass, which would be further decreased to a lower level by the high light. Based on above mentioned analysis, to decrease the MCYST production of Microcystis blooms, we should control nutrient, especial nitrogen through pollutant intercepting and increase the light intensity through improving water transparency. (C) 2019 Elsevier Ltd. All rights reserved.