In this review, the system of multi-level collagen aggregates including collagen molecular, collagen fiber, advanced collagen aggregates, and tissues was reviewed. The preparation methods of multi-level collagen aggregates were introduced, and the relationship between structure and properties of them was analyzed and clarified. The general rule of structure-activity relationship of multi-level collagen aggregates under different modifiers and modified conditions was analyzed, and a theoretical basis for the application of multi-level collagen aggregates in biomedical field was provided. Finally, the applications of a series of biomedical materials of multi-level collagen aggregates and their modified products were listed. It is confirmed that the application field of multi-level collagen aggregates and their modified products might be far greater than collagen and other biomass. The multi-level collagen aggregates might have a very broad application prospect.