Microplastics (MPs) are an emerging threat to ecological conservation and biodiversity; however, little is known of the types and possible impacts of MPs in pollinators. To examine whether MPs were present in honeybees, we analyzed the honeybee samples collected in fields from six provinces in China. Four types MPs were identified in honeybee including polystyrene (PS) by Raman spectroscopic analysis, and these plastic polymers were detected in 66.7% bee samples. Then, we assessed the physical and biological impacts of PS of three sizes (0.5, 5, and 50 μm) on bees for 21 days. Next, we measured how the presence of PS affected the Israeli acute paralysis virus proliferation, a small RNA virus associated with bee colony decline. Experimental evidence showed that a large mass of PS was ingested and accumulated within the midgut and enhanced the susceptibility of bees to viral infection. Not only histological analysis showed that PS, especially 0.5 μm PS, damaged the midgut tissue and was subsequently transferred to the hemolymph, trachea, and Malpighian tubules, but also qPCR and transcriptomic results indicated that genes correlated with membrane lipid metabolism, immune response, detoxification, and the respiratory system were significantly regulated after PS ingestion. Our results highlight neglected MP contamination to the bees, a pollination ecosystem stressed by the anthropogenic pollution, and have implications for human health via ingestion of bee products.