Microplastics (MPs) as widespread contamination pose a high risk for aquatic organisms. Due to hard-to-degrade components and properties, e.g., size, MPs can accumulate in the intestines of aquatic organisms and cause physical damage and inflammatory responses. However, current approaches for understanding the adverse effects of MPs are based on cell population-averaged measurements, which might obscure the critical contributions of individual cell populations. Our aim was to gain a comprehensive understanding of the size-dependent effects of polystyrene MPs (PS-MPs) on intestinal cell populations in zebrafish and characterize the interplay of MPs, intestinal cells and intestinal microbiota. Here, we used single-cell RNA sequencing to determine the transcriptome heterogeneity of 12000 intestinal cells obtained from zebrafish exposed to 100-nm, 5-μm and 200-μm PS-MPs for 21 days. Eight intestinal cell populations were identified, including enterocytes, secretory cells (enteroendocrine and goblet cells), lymphocytes (T cells and B cells) and phagocytes (M1 macrophages, M2 macrophages and neutrophils). Combined with changes in intestinal microbiota, our findings highlight a previously unrecognized endpoint that all three sizes of PS-MPs induced dysfunction of intestinal immune cells (including effects on phagosomes and regulation of immune system processes) and increased the abundance of pathogenic bacteria. However, only 100-nm PS-MPs altered expression of genes related to phagocyte-produced ROS generation and increased mucus secretion by secretory cells. Microsize PS-MPs specifically changed the lysosome (5 μm) and cell surface receptor signaling (200 μm) processes of macrophages. This study for the first time shows the feasibility of using scRNA-seq to investigate the heterogeneity of zebrafish intestinal cells in response to MPs, and our findings pinpoint to cell-specific and size-dependent responses to PS-MPs in fish intestine, which can provide a reference for future study directions.