A system and a method for preprocessing capsule endoscope images are provided. The capsule endoscopic image preprocessing system include an in vitro image removal module, an invalid image removal module, a digestive tract image classification module, a lesion and anatomical structure identification module, and a lesion and anatomical structure redundant image removal module. The capsule endoscopic image preprocessing system removes in vitro images and invalid images from capsule endoscopic images, classifies the capsule endoscopic images according to different parts of the digestive tract, identifies lesion and anatomical structures in the classified capsule endoscopic images; and removes redundant lesion and anatomical structure images according to the lesion and anatomical structures.