Background: The diagnosis of Crohn’s disease (CD) is still challenging, and the search for novel biomarkers is a worthwhile endeavor. Mast cells can be activated in various ways. Whether serum IgE, anti-IgE and anti-IgE high-affinity receptor (FcεRI) antibodies are involved in the pathogenesis of CD was investigated by bridging FcεRI to activate MCs. The relationship between MCs and CD is also explored in this research.Methods: Microplates with human FcεRIα were coated and an enzyme-labeled anti-human IgG was used as the tracer to successfully establish an indirect enzyme-linked immunosorbent assay (ELISA) method for semi-detection of IgG anti-FcεRI. The optimal working conditions were explored, followed by conducting the method evaluation. The serum samples and clinical data of 117 CD patients and 75 healthy controls were collected. IgE was measured by the rate turbidity turbidimetry; IgG anti-IgE and IgG anti-FcεRI were detected by ELISA. IgG anti-pancreatic antibody (PAB) and anti-Saccharomyces cerevisiae antibody (ASCA) were determined by indirect immunofluorescence assay. Data were analyzed concerning the clinical characteristics.Conclusions: An ELISA for the detection of anti-FcεRI was established and validated, which may contribute to facilitating the study of mast cell-related diseases. Anti-FcεRI positive CD patients were associated with adverse phenotypes, suggesting its value in the diagnosis and management of CD.