Although gut seasonal plasticity has been extensively reported, studies on physiological flexibility, such as water-salt transportation and motility in reptiles, are limited. Therefore, this study investigated the intestinal histology and gene expression involved in water-salt transport (AQP1, AQP3, NCC, and NKCC2) and motility regulation (nNOS, CHRM2, and ADRB2) in desert-dwelling Eremias multiocellata during winter (hibernating period) and summer (active period). The results showed that mucosal thickness, the villus width and height, the enterocyte height of the small intestine, and the mucosal and submucosal thicknesses of the large intestine were greater in winter than in summer. However, submucosal thickness of the small intestine and muscularis thickness of the large intestine were lower in winter than in summer. Furthermore, AQP1, AQP3, NCC, nNOS, CHRM2, and ADRB2 expressions in the small intestine were higher in winter than in summer; AQP1, AQP3, and nNOS expressions in the large intestine were lower in winter than in summer, with the upregulation of NCC and CHRM2 expressions; no significant seasonal differences were found in intestinal NKCC2 expression. These results suggest that (i) intestinal water-salt transport activity is flexible during seasonal changes where AQP1, AQP3 and NCC play a vital role, (ii) the intestinal motilities are attenuated through the concerted regulation of nNOS, CHRM2, and ADRB2, and (iii) the physiological flexibility of the small and large intestine may be discrepant due to their functional differences. This study reveals the intestinal regulation and adaptation mechanisms in E. multiocellata in response to the hibernation season.