The invention discloses an antigen-free collagen aggregate and a preparation method thereof. The preparation method is characterized by comprising the following steps: with traceable animal skin or tendo calcaneus as a raw material, performing operations by the process such as fleshing, stripping fascia, degreasing, removing foreign protein and decellularizing; performing fine purification on the animal skin or tendo calcaneus, and then carrying out separation and purification on the collagen aggregate by the methods of acid fluffing, homogenizing, salting out for a plurality of times, centrifuging for a plurality of times and the like, thereby finally obtaining the antigen-free collagen aggregate. The collagen aggregate is a mixture of a collagen fiber and a collagen bundle, and has a periodic light and shade horizontal grain structure; and the space between the horizontal grains is about 67nm. The material has good biocompatibility, biodegradability, mechanical property and hemostatic performance, also has the characteristics of low antigenicity, biological activity and the like, and can be widely applied to preparation of biomedical materials such as a hemostatic material, a tissue engineering material, a biological dressing, a biodegradable medical suture and a plastic material.