Abstract: Cyanobacterial toxin of β-N-methylamino-L-alanine (BMAA) which possesses chronic neurotoxicity, biological accumulation and biological amplification effects will seriously affect the normal growth, development and reproduction of the aquatic organisms, especially related to the problem of food quality and safety of aquatic products in the freshwater aquaculture ecosystem. Therefore, the attention and investigation on the pollution characteristics of BMAA and its health risk assessment, as well as the research and exploitation of efficient, safe control technology of BMAA pollution are particularly urgent and desperately needed. In order to know more about the pollution levels of BMAA in freshwater aquaculture ecosystem, this paper selected the typical freshwater aquaculture pond water, sediment and six kinds of aquatic products (Corbicula fluminea, Bellamya aeruginosa, Macrobrachium nipponense, Eriocheir sinensis, Mylopharyngodon piceus and Carassius auratus) as the study objects to detect their contents of BMAA used the method of HPLC-MS/MS, and on this basis, the risk assessment of human health by BMAA was carried out by using the health risk assessment methods proposed by the National Academy of Sciences. At the same time, using L-cysteine modified GO as the carrier, combined with the allelochemical “gallic acid” to prepare a novel allelopathic slow-released algal inhibition agent, in order to study the effect of its algal inhibition and control of BMAA toxin pollution. The results showed that the average BMAA concentrations in the edible portions of the six freshwater aquatic products were from (0.364±0.006) to (1.040±0.025) μg/g, the guidance values of BMAA based on the quality and safety of freshwater aquatic products were proposed to be 12 μg/g for adults and 3 μg/g for children. And the EDI value (estimated daily intake) of BMAA in the above six aquatic products was much lower than the TDI value (allowable daily intake), and the concentration of BMAA was also much lower than the GV value (recommended safety limit), which can be concluded that the risk to human health by BMAA was low. The novel allelopathic slow-released algal inhibition agent prepared with the concentration of 12.5 mg/L could not only guarantee the better antialgal effect, but also effectively control the toxin pollution of BMAA. After adding the novel allelopathic slow-released algal inhibition agent 7 days, the content of intracellular BMAA decreased significantly, while the increase of extracellular BMAA was not significant, and the total amount of BMAA decreased by 69.72%. The biological acute toxicity test showed that the novel allelopathic slow-released algal inhibition agent had no obvious toxic effects on Daphnia magna and zebrafish, so it had good ecological safety and could be applied to the treatment of water bloom in the aquaculture pond.