Microplastics and the antibiotic sulfamethazine (SMZ) are two prevalent pollutants in regions with high human activity, particularly in coastal marine environments. In this study, the individual and joint effects of microplastics (i.e., the bio-based microplastics polylactic acid (PLA), the petroleum-based microplastics polyethylene terephthalate (PET), and the petroleum-based microplastics polystyrene (PS) at 0.5 and 5 mg/g) and sulfamethazine (SMZ, at 5 mg/g) on the gut microbiota of marine medaka (Oryzias melastigma) via dietary route were investigated. For the individual microplastics exposure, two petroleum-based microplastics PET and PS significantly decreased the alpha diversity and the complexity of co-occurrence networks of gut microbiota. Differently, the adverse effects caused by the bio-based microplastic PLA were more modest, suggesting that PLA was less hazardous than PET and PS. For the combined exposure, SMZ alone dramatically impaired the homeostasis of gut microbiota by decreasing the alpha diversity and the complexity of co-occurrence networks, while the presence of PLA or PET alleviated these adverse effects caused by SMZ. Interestingly, such an alleviation effect was not observed in the SMZ + PS groups, suggesting that different types of microplastics might exhibit distinct joint effects with SMZ. Our findings contribute to a better understanding of the ecological risk of different types of microplastics to marine ecosystems, especially in a scenario of combined pollution with antibiotics.