The invention relates to a loaded aprepitant nanocrystal lipid microcapsule and a preparation method thereof, and belongs to the technical field of a medicine. The microcapsule is prepared by the method comprising the following steps: preparing an aprepitant nanocrystal from aprepitant by virtue of a grinding process, high-speed air jet pulverization or high-pressure homogenization, then mixing and emulsifying the aprepitant nanocrystal with phospholipid, removing a liquid phase and drying so as to obtain the aprepitant nanocrystal lipid microcapsule. The prepared loaded aprepitant nanocrystal lipid microcapsule can improve the stability of the aprepitant nanocrystal and the lipid loaded nanocrystal can increase the speed and the amount of being absorbed by gastrointestinal mucosa of a body, so that the effects of relatively high bioavailability and accelerated development of efficacy are achieved; and the preparation method of the loaded aprepitant nanocrystal lipid microcapsule is mild in condition, simple and controllable, low in preparation cost and is suitable for large-scale production.