The gut microbiota has been considered one of the key factors in host health, which is influenced by many environmental factors. The geomagnetic field (GMF) represents one of the important environmental conditions for living organisms. Previous studies have shown that the elimination of GMF, the so‐called hypomagnetic field (HMF), could affect the physiological functions and resistance to antibiotics of some microorganisms. However, whether long‐term HMF exposure could alter the gut microbiota to some extent in mammals remains unclear. Here, we investigated the effects of long‐term (8‐ and 12‐week) HMF exposure on the gut microbiota in C57BL/6J mice. Our results clearly showed that 8‐week HMF significantly affected the diversity and function of the mouse gut microbiota. Compared with the GMF group, the concentrations of short‐chain fatty acids tended to decrease in the HMF group. Immunofluorescence analysis showed that HMF promoted colonic cell proliferation, concomitant with an increased level of reactive oxygen species (ROS). To our knowledge, this is the first in vivo finding that long‐term HMF exposure could affect the mouse gut microbiota, ROS levels, and colonic cell proliferation in the colon. Moreover, the changes in gut microbiota can be restored by returning mice to the GMF environment, thus the possible harm to the microbiota caused by HMF exposure can be alleviated. © 2022 Bioelectromagnetics Society.