With the increasing concern of cyanobacterial blooms, numerous techniques have been developed to mitigate these environmental nuisances. During bloom control, the allelopathic effects of compounds released from cyanobacterial cells are considered as secondary hazards. In this study, the findings indicated that Microcystis lysate inhibited algal proliferation and disrupted the development of zebrafish embryos. Then, allelochemicals in Microcystis lysate were identified using gas chromatography-mass spectrometry, with 2, 4-di-tert-butylphenol (2, 4-DTBP) being the only identified phenol, which was selected for further study. The results showed that 2,4-DTBP caused oxidative damages, disrupted metabolic activity, and suppressed photosynthetic activity, consequently impeding the growth of Microcystis aeruginosa (M. aeruginosa) and Chlorella pyrenoidosa (C. pyrenoidosa). Moreover, it enhanced the interspecies competitive advantages of M. aeruginosa by increasing phosphate uptake rate. Furthermore, at a concentration of 2 mg L−1, 2, 4-DTBP negatively affected the development of zebrafish embryos, manifesting in mortality, malformation, and hatching delay. Therefore, the investigation identified 2, 4-DTBP as a potential allelochemical within Microcystis lysate. Although the effective concentration for freshwater algae and zebrafish embryos was higher than that found in Microcystis lysate, it highlighted the need for careful monitoring of aquatic ecosystem health during cyanobacterial bloom mitigation.