Environmental conditions, including enrichment and stress, affect animal behaviors, but limited information is available regarding the differences in animal functions between the chamber (ventilated system) vs. IVC (individually ventilated cages) housing systems. Therefore, the effects of different housing systems were examined on physical, emotional, and cognitive functions and the intestinal flora with aging. DBA/2CrSlc mice were divided into chamber and IVC groups. Differences in the structure of the two cages considered whether the mouse could dangle or not. Physical, emotional, and cognitive functions were examined using the open field, black and white box, object recognition, horizontal bar, wire hanging, balancing, footprint, and locomotor tests. The IVC group demonstrated significantly less food intake, higher body weight (by approximately 5 g), lower rectal core temperature, less muscle and balancing powers with aging, and fewer anxiety-like behaviors than the chamber group. No differences were observed in the cognitive function and intestinal microbiota between the groups. The housing environment affected the rodent basal temperature and body weight as well as the physical and emotional functions. Scientists should be attentive to the type of cages used in the housing system for an experiment, especially when comparing the results with animals reared in different systems.