Intestinal diseases seriously affect the quality of life. The assays for intestinal disease study based on two‐dimensional in vitro cell culture and animal models fail to model human physiology and pathophysiology accurately. As a bridge between in vitro cell culture and clinical pathological specimens, intestine‐on‐a‐chip lined with living cells under dynamic flow can recapitulate the human intestinal microenvironment with high precision. Here, we summarize important elements for reconstructing the intestinal microenvironment and the mostly used intestine‐on‐a‐chip models that simulate the basic intestinal microenvironment, and the intestinal microenvironment with pathogenic bacteria, probiotic bacteria, viruses, tumor cells, and parasites. We also introduce the commonly used analytical techniques, including immunofluorescence imaging, mass spectrometry, DNA/RNA‐based analysis, and electrochemistry, which can be integrated with intestine chips for intestinal microenvironment characterization. We further review the application of intestine‐on‐a‐chip for intestinal disease study and pharmacological research. Finally, we discuss the application prospects and challenges of intestine chips in biomedical and clinical research.