Changes of several trace elements have been reported to contribute to the pathogenesis of Crohn's disease (CD), which is associated with gut microbiota imbalance. This study aimed to investigate changes in trace elements in Chinese CD patients, and explore the correlation of trace element status with clinical features and gut microbiota. Eighty CD patients and 45 healthy volunteers were enrolled between July 2022 and November 2022. Serum zinc, copper, magnesium and selenium were measured by inductively coupled plasma mass spectrometry. The nutritional status was assessed based on body mass index and albumin and disease severity was determined according to the Crohn's disease activity index and C-reactive protein. Fecal gut microbiota was analyzed using 16SrRNA gene sequencing. Compared with healthy controls, serum copper increased, but serum selenium reduced in Chinese CD patients. The serum levels of selenium and magnesium were positively related to nutritional status, and the serum levels of selenium and copper were associated with disease severity. Selenium deficiency in CD patients was closely related to the diversity and abundance of gut microbiota. The serum levels of several trace elements change in the CD patients and are associated with nutritional status and disease severity. Selenium deficiency in CD patients is associated with the diversity of gut microbiota, suggesting an interaction between trace elements and gut microbiota.