This study investigated the effects of nanoplastics on marine organisms via trophic transfer in the food chain. We designed a three-step food chain comprising microalga (Dunaliella salina), small crustaceans (Artemia franciscana), and fish (small yellow croakers; Larimichthys polyactis) and evaluated the effects of trophic transfer in marine organisms, as well as verified the possibility of nanoplastic transfer to humans via trophic transfer. Using amine-modified nanopolystyrene (nPS-NH2) as a pollutant, we conducted both direct-exposure and trophic transfer experiments to determine how pollutants move through the food chain (D. salina → A. franciscana). Exposure of D. salina to nPS-NH2, which was adsorbed on its cell wall, resulted in transfer to A. franciscana with alteration of gut permeability. Additionally, assessment of the adverse effects of nPS-NH2 via a dietary pathway (three-step food chain) on the L. polyactis digestive system revealed that nanoplastics adsorbed to the cell wall of microalgae are gradually transferred to higher trophic level organisms, such as via food resources consumed by humans, inducing the inhibition of digestive enzyme activity (α-amylase). It indicates that human could eventually be exposed to nanoplastics and experience toxicity.