Microplastics (MPs) and fluoxetine are ubiquitous emerging pollutants in aquatic environments that may interact with each other due to the carrier effects of MPs, posing unpredictable risks to non-target organisms. However, limited studies have focused on the carrier effects of MPs in the aquatic food chain. This study evaluated the influences of polystyrene MPs on the trophic transfer and biotoxicity of fluoxetine in a simple food chain composed of brine shrimp (Artemia nauplii) and zebrafish (Danio rerio). The finding reveals that carrier effects of MPs enhanced the accumulation of waterborne fluoxetine in brine shrimp, but suppressed that in zebrafish due to the distinct retention times. The accumulated fluoxetine in shrimp was further transferred to fish through the food chain, which was alleviated by MPs due to their cleaning effects. In addition, the specific neurotransmission biotoxicity in fish induced by fluoxetine was mitigated by MPs, whilst the oxidative damage, apoptosis, and immune responses in zebrafish were reversely enhanced by MPs due to the stimulating effect. These findings highlight the alleviating effects of MPs on the trophic transfer and specific biotoxicity of fluoxetine in the food chain, providing new insights into the carrier effects of MPs in aquatic environments in the context of increasing global MP pollution.