Wet precipitation, as an important process of geochemical cycling and the most effective way of cleaning fine atmospheric particles (PM_2.5), can introduce the toxic substances in the atmosphere into the water environment. The adverse effect of wet precipitation of PM_2.5 on marine fish is still unclear. In this study, PM_2.5 samples were collected from six locations along coastal areas of the south China sea for 30 days and used to simulate the impacts of multiday discontinuity wet precipitation of PM_2.5 on marine medaka (Oryzias melastigma) in the case of 30 days discontinuity heavy rain (rainfall ≥ 7.6 mm/h and persist 1 h each day). Results showed that wet precipitation of PM_2.5 significantly inhibited the body weight gain of fish. In accordance, the size and number of lipid droplets in liver of the exposed groups were lower than those in normal control (NC) group. The expressions of genes involving in lipid degradation including lipoprotein lipase gene (LPL) and carnitine palmitoyltransferase gene (CPT) were up-regulated after exposure. The composition, diversity and function of gut microbiome were affected by wet precipitation of PM_2.5. PM_2.5 from industrial areas that have higher concentrations of metal profiles show more obvious impacts than PM_2.5 from agricultural leisure areas that possessed lower concentrations. All together, the results indicated that wet precipitation of PM_2.5 can decrease the diversity of gut microbiome, affect the lipid metabolism, and finally suppress the growth of marine medaka. It confirmed the potential ecological risks of long-term rainfall in air pollution areas to the aquatic organisms.