Microplastic (MP) has become a concerning global environmental problem. It is toxic to aquatic organisms and can spread through the food chain to ultimately pose a threat to humans. In the environment, MP can interact with microbes and act as a microbial habitat. However, effects of polystyrene MP on the gut microbiota in mammals remain unclear. Here, male mice were exposed to two different sizes of polystyrene MP for 5 weeks to explore its effect. We observed that oral exposure to 1000 μg/L of 0.5 and 50 μm polystyrene MP decreased the body, liver and lipid weights in mice. Mucus secretion in the gut decreased in both sizes of polystyrene MP-treated groups. Regarding the gut microbiota, at the phylum level, polystyrene MP exposure decreased the relative abundances of Firmicutes and α- Proteobacteria in the feces. Furthermore, high throughput sequencing of the V3-V4 region of the 16S rRNA gene revealed significant changes in the richness and diversity of the gut microbiota in the cecums of polystyrene MP-treated mice. At the genus level, a total of 6 and 8 types of bacteria changed in the 0.5 and 50 μm polystyrene MP-treated groups, respectively. Furthermore, an operational taxonomic unit (OTU) analysis identified that 310 and 160 gut microbes were changed in the 0.5 and 50 μm polystyrene MP-treated groups, respectively. In addition, the hepatic triglyceride (TG) and total cholesterol (TCH) levels decreased in both 1000 μg/L 0.5 and 50 μm polystyrene MP-treated groups. Correspondingly, the relative mRNA levels of some key genes related to lipogenesis and TG synthesis decreased in the liver and epididymal fat. These results indicated that polystyrene MP could modify the gut microbiota composition and induce hepatic lipid disorder in mice; while the mouse is a common mammal model, consequently, the health risks of MP to animals should not be ignored.