Flocoumafen (FCF), a second-generation anticoagulant rodenticide (SGAR), has limited toxicological data regarding its effects on aquatic organisms. In this study, we exposed zebrafish embryos to FCF solutions at concentrations of 0.2, 0.4, and 0.8 mg/L until 120 h post-fertilization (hpf). The results revealed a decrease in survival rates. Notably, FCF exposure significantly reduced the frequency of spontaneous tail coils at 24 hpf, while shortened body length and induced spinal curvature at 120 hpf. Furthermore, zebrafish larvae exhibited craniofacial abnormalities and incomplete bone mineralization at 120 hpf following FCF exposure. In Tg(HuC:EGFP) transgenic strains, neuronal loss was observed. Additionally, FCF-exposed zebrafish larvae showed a marked reduction in locomotor ability, activity levels, and turning capacity. The qPCR and enzyme activity assays revealed significant changes in gene expression associated with the Notch signaling pathway, accompanied by increased levels of reactive oxygen species (ROS), superoxide dismutase (SOD), catalase (CAT), malondialdehyde (MDA). Astaxanthin (ASTA) partially alleviated the toxicities induced by FCF. These findings suggest that FCF may induce skeletal and neurological toxicities by affecting oxidative stress, disrupting the normal expression of skeletal and nervous system-related genes in the Notch signaling pathway, and ultimately leading to behavioral abnormalities. Our findings may provide new insights into a comprehensive evaluation of FCF toxicology in aquatic organisms, and may assist the government in formulating and implementing regulatory policies regarding the application of FCF.