The co-existence of microplastics (MPs) and methamphetamine (METH) in aquatic ecosystems has been widely reported; however, the joint toxicity and associated mechanisms remain unclear. Here, zebrafish larvae were exposed individually or jointly to polystyrene (PS) and polyvinyl chloride (PVC) MPs (20 mg/L) and METH (1 and 5 mg/L) for 10 days. The mortality, behavioral functions, and histopathology of fish from different groups were determined. PS MPs posed a stronger lethal risk to fish than PVC MPs, while the addition of METH at 5 mg/L significantly increased mortality. Obvious deposition of MPs was observed in the larvae's intestinal tract in the exposure groups. Meanwhile, treatment with MPs induced intestinal deposits and intestinal hydrops in the fish, and this effect was enhanced with the addition of METH. Furthermore, MPs significantly suppressed the locomotor activation of zebrafish larvae, showing extended immobility duration and lower velocity. METH stimulated the outcome of PS but had no effect on the fish exposed to PVC. However, combined exposure to MPs and METH significantly increased the turn angle, which declined in individual MP exposure groups. RNA sequencing and gene quantitative analysis demonstrated that exposure to PS MPs and METH activated the MAPK signaling pathway and the C-type lectin signaling pathway of fish, while joint exposure to PVC MPs and METH stimulated steroid hormone synthesis pathways and the C-type lectin signaling pathway in zebrafish, contributing to cellular apoptosis and immune responses. This study contributes to the understanding of the joint toxicity of microplastics and pharmaceuticals to zebrafish, highlighting the significance of mitigating microplastic pollution to preserve the health of aquatic organisms and human beings.