The ubiquity of microplastics in the world's ocean has aroused great concern. However, the ecological effects of microplastics at environmentally realistic concentrations are unclear. Here we showed that exposure of marine medaka (Oryzias melastigma) to environmentally relevant concentrations of 10 μm polystyrene microplastics for 60 days not only led to microplastic accumulation in the gill, intestine, and liver, but also caused oxidative stress and histological changes. Moreover, 2, 20, and 200 μg/L microplastics delayed gonad maturation and decreased the fecundity of female fish. Alterations of the hypothalamus-pituitary-gonadal (HPG) axis were investigated to reveal the underlying mechanisms, and gene transcription analysis showed that microplastic exposure had significantly negative regulatory effects in female HPG axis. Transcription of genes involved in the steroidogenesis pathway in females were also downregulated. This disruption resulted in decreased concentrations of 17β-estradiol (E2) and testosterone (T) in female plasma. Furthermore, parental exposure to 20 μg/L microplastics postponed the incubation time and decreased the hatching rate, heart rate, and body length of the offspring. Overall, the present study demonstrated for the first time that environmentally relevant concentrations of microplastics had adverse effects on the reproduction of marine medaka and might pose a potential threat to marine fish populations.