The rhythmic fluctuations of biological activities with the rotation of the earth for nearly 24 h are called circadian clock. Intestinal flora is a community of microorganisms that live in the gastrointestinal tract of human body, and its balance plays an important role in maintaining homeostasis. Specific environment changes in the external environments (such as special circadian rhythms in the polar region and high-altitude hypoxia in the plateau region) and changes in lifestyle (such as shift work, insomnia, and flights across time zones) can adversely affect circadian rhythms and lead to disruption of the circadian clock and intestinal flora. The synergistic effects of circadian clock disruption and dysbiosis further lead to an imbalance of homeostasis of body internal environment, which increases the risk of metabolic disorders. Elucidating the changes of circadian clock and intestinal flora in special environments may provide new ideas for the maintenance of circadian rhythms and homeostasis in special environments.