In some small mammals, digestive tract morphology is known to vary between and within individuals over time. Although changes in organs such as the stomach, small intestine, cecum, and large intestine vary among species, there is a trend toward increasing length and mass in individuals faced with increasing energy demands due to cold exposure or to reduced food quality. These morphological changes can also be induced by short day photoperiod, and could therefore serve as a winter adaptation. However, the extent to which these morphological responses to environmental cues are shared among mammals is not known. We examined the influence of cold temperature and short day photoperiod on the digestive tract morphology of Apodemus speciosus. The length and dry mass of all organs increased in response to cold temperature, and the dry mass of the small intestine was also increased by short day photoperiod. The small intestine is the principal site of nutrient absorption, and changes in its morphology may be an important aspect of winter adaptation. These results suggest that digestive tract morphology may alter flexibly as a means of coping with energy challenges.