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With the growing dependence on lithium-ion batteries, there is an urgent need to understand the potential developmental toxicity of LiPF₆, a key component of these batteries. Although lithium’s toxicity is well-established, the biological toxicity of LiPF₆ has been minimally explored. This study leverages the zebrafish model to investigate the developmental impact of LiPF₆ exposure. We observed morphological abnormalities, reduced spontaneous movement, and decreased hatching and swim bladder inflation rates in zebrafish embryos, effects that intensified with higher LiPF₆ concentrations. Whole-mount in situ hybridization demonstrated that the specific expression of the swim bladder outer mesothelium marker anxa5b was suppressed in the swim bladder region under LiPF₆ exposure. Transcriptomic analysis disclosed an upregulation of apoptosis-related gene sets. Acridine orange staining further supported significant induction of apoptosis. These findings underscore the environmental and health risks of LiPF₆ exposure and highlight the necessity for improved waste management strategies for lithium-ion batteries.