The present invention relates to a pharmaceutical composition, and to a food composition, for regulating the motility of the gastrointestinal tract, and more particularly, to a pharmaceutical composition, and to a food composition, which use a Chamaecyparis obtusa extract so as to be effective in the prevention and treatment of motility disorders of the gastrointestinal tract. The pharmaceutical composition for regulating the motility of the gastrointestinal tract according to the present invention contains the Chamaecyparis obtusa extract as an active ingredient, wherein the motility of the gastrointestinal tract is regulated by varying the electrical activity of interstitial cells of Cajal. Further, the food composition for regulating the motility of the gastrointestinal tract according to the present invention contains the Chamaecyparis obtusa extract as an active ingredient.