Organisms constantly ingest microplastics directly from the environment or indirectly via trophic transfer due to the pervasiveness of microplastic pollution. However, most previous studies have only focused on waterborne exposure at the individual level, while few studies have investigated the contribution of trophic transfer to the exposure in organisms. We comprehensively evaluated the differences in microplastic ingestion and toxic effects in zebrafish exposed to microplastics via two concurrent routes (waterborne and foodborne). The polyethylene microplastics (40-47 μm, 0.1-10 mg/L) concentration used here was set in a range closed to the environmentally relevant microplastic concentrations, especially considering the extreme high concentration scenarios in wastewater. The concentration of microplastics resulting from foodborne exposure (0.01±0.01 μg/mg; 0.1±0.1 particles/mg) was significantly lower than that through waterborne exposure (0.06±0.02 μg/mg; 0.8±0.3 particles/mg), suggesting the ingestion of microplastics in their tissues occurs mainly through direct environmental uptake rather than food chain transfer (though the initial microplastic concentration was 1000 folds lower). However, more sublethal impacts, including the significant abnormal hyperactive swimming behaviour (107±5% induction; p< 0.05), were observed in the foodborne group than waterborne group. Additionally, ingenuity pathway analysis predicted both exposure routes caused obvious nervous system interference but through opposite modes of action. This was further verified by the alteration of neurotransmitter biomarkers that neurotoxicity mechanisms were completely different for the two exposure routes. The neurotoxic effects of microplastics are non-negligible and can exert together through both water- and foodborne exposure routes, which deserves further attention.