Triclosan (TCS), a common antimicrobial agent, is widely detected in the global environments nowadays globally. Using marine medaka as a model, this study investigated and compared the transgenerational and multigenerational neurotoxic effects on fish. The environmentally realistic concentration of TCS can induce hyperlocomotor activities and increase heart rate, while higher concentrations (>500 μg/L) can inhibit hatching and cause cardiovascular malformations and neurotransmitter imbalances. Parental (F0) exposure to TCS resulted in transgenerational effects on locomotor activities manifested in F2, alongside with alterations in phototransduction and cell adhesion pathways. Global DNA methylation analyses indicated that the observed transgenerational effects are mediated through relevant epigenetic changes. Multigenerational exposure to TCS increased locomotor activities from F1 to F3, which is associated with changes in the expression of genes related to eye structure, phototransduction, and lipid and retinol metabolisms, thereby affecting energy metabolism and visual function. Results of this study highlight the difference between transgenerational and multigenerational effects of TCS exposure, and potential biases incurred in current risk assessment based exclusively on data derived from F0, which presents challenges for environmental management and regulatory standards.