The adverse effects of microplastics ingested by aquatic organisms have been reported previously. However, most studies are primarily qualitative; therefore, it is challenging to determine the direct interactions between microplastics and organisms. In this study, for the first time, the microplastic intake behavior of silver carp (Hypophthalmichthys molitrix) larvae, a popular fish in China, as well as intestine accumulation and excretion of the microplastics were quantitatively investigated. The results showed that the intake of microplastics by silver carp larvae was negatively correlated with the particle size of microplastics but positively correlated with the exposure concentration. After intaking microplastics of different sizes, small-sized microplastics (≤ 150 μm) were rapidly excreted from the intestine of silver carp, whereas some large-sized microplastics (≥ 300 μm) remained in the intestine for a long time. The presence of food significantly increased the intake of large-sized microplastics, while small-sized microplastics intake was unaffected by the food. More importantly, the ingested microplastics caused specific changes in the diversity of intestinal microflora, potentially leading to abnormal immune and metabolic functions. The results of this study provide a new understanding on the potential impacts of microplastics on aquatic organisms.