Cyanobacterial blooms are a global ecological problem. The purpose of this study is to find microbial strains that can be used for the biological control of cyanobacterial blooms. In this study, a strain of Lysinibacillus fusiformis (QY-12) with the best algae inhibition effect was isolated and screened. The inhibition rate of Microcystis aeruginosa in the growth index period was 82.01% after 8 days of interference by QY-12. The algicidal substance l-2-aminoadipic acid (L-2-AA) produced by QY-12 was purified via preparative HPLC and identified by nuclear magnetic resonance (NMR), liquid chromatography-mass spectrometry (LC-MS) and infrared spectroscopy (IR). It was found by scanning electron microscopy that L-2-AA had a significant inhibitory effect on Microcystis aeruginosa in the early and middle stages of growth. This study provides a new idea for the prevention and control of cyanobacterial blooms.