The development of functional contrast agents for diagnosis and therapy of functional gastrointestinal disorders has been a focus of research in recent years. Owing to the excellent distribution and function of 5-HT3 in gastrointestinal mucosa, a novel magnetic contrast agent (AH-CTS-Gd nanosphere) was prepared based on chitosan and 5-HT3 receptors, which realize multifunctional assessment of gastric emptying and gastrointestinal mucosa-targeted MR imaging. The obtained AH-CTS-Gd nanosphere was administered orally to avoid potential toxicity from intravenous administration of a high dose. The results showed that a suitable gastric emptying time and clear gastrointestinal mucosa structure can be observed using the obtained AH-CTS-Gd nanosphere. Immunofluorescence and TEM images of gastrointestinal mucosa suggested a strong combination of the AH-CTS-Gd nanosphere with gastrointestinal mucosa because chitosan and Anti-5-HT3R can combine with gastrointestinal mucosa through electrostatic adherence and antigen-antibody binding. This technology has potential applications in the examination of functional gastrointestinal diseases, without affecting the detection of gastric emptying, possibly enhancing mucosal imaging.