Microplastics are plastic fragments widely distributed in the environment and accumulate in the organisms. However, the research on microplastics effects in mammals is limited. Polyethylene is the main kind of microplastics in the environment. We hypothesized that polyethylene exposure disrupts host intestine metabolism by modifying intestine microflora composition and then lipopolysaccharide (LPS) pathway. Female mice were orally exposed to 0, 0.002 and 0.2 μg/g/d polyethylene microplastics (PE MPs) for 30 days. Colon mucin density was quantized after AB-PAS staining. Mucin 2 (MUC2), inflammatory factors (IL-1β, IL-6, IL-8 and IL-10), short-chain fatty acid receptors (GPR41 and GPR43), LPS receptors (TLR4 and MyD88) and LPS pathway downstream genes (ERK1 and NF-κB) mRNA levels in colon were measured. Feces were collected on the 15th day of exposure for gut microflora analysis. Blood biochemical analysis was performed. Results showed that 0.2 μg/g/d PE MPs exposure significantly decreased colon mucin expression (p < 0.05), decreased IL-1β (p < 0.05) and increased IL-8 and IL-10 levels (p < 0.01 and p < 0.001 respectively). Microflora data showed that in 0.2 μg/g/d PE MPs group the number of Firmicutes decreased and the number of Bacteroides increased (both p < 0.01). Predicted KEGG metabolic pathways by piecrust method indicated that PE MPs enhanced amino acids metabolism in microflora. ERK1 and NF-κB mRNA were significantly lower in 0.2 μg/g/d PE MPs group (both p < 0.001). Blood total protein, albumin and globulin levels significantly increased after 0.2 μg/g/d PE MPs exposure (p < 0.01, p < 0.01 and p < 0.05 respectively). These results indicate that PE MPs exposure induced decreased mucin production, a slight immune response and increased the microflora amino acid metabolism in the mice colon by modifying colon microflora composition. Polyethylene microplastics exposure decreased colon mucin release and increased amino acid metabolism by modifying colon microflora composition. Display omitted •PE MPs exposure caused a decrease of colon mucin secretion in mice colon.•PE MPs exposure induced a mild inflammatory response in the colonic epithelium.•PE MPs exposure decreased the Firmicutes and increased the Bacteroides in gut microflora.•Alternation of microflora composition induced by PE MPs increased amino acid metabolism.•Both blood albumin and globulin levels increased after PE MPs exposure.