Exploration of the denaturation and refolding of natural collagen is important for the application of collagen and its denatured products. In this study, using urea as a denaturant, we prepared a denatured natural collagen product and analyzed its structural changes. The denaturation treatment severely destroyed the triple helix conformation of collagen, but had no significant effect on the primary structure of its α chains or the covalent cross-linking between α chains. Next, we observed the refolding behavior of the denatured collagen by removing urea through dialysis. We found that the denatured collagen products from different sources (grass carp skin, bovine tendon) all showed a reconstruction of the triple helix conformation up to 60-75% of the value of natural collagen during the refolding process. The telopeptide did not significantly promote triple helix reconstruction. In conclusion, the reconstruction of the α chains did not perfectly occur in a “head-to-head, tail-to-tail” manner in refolded collagen, as each α chain was participating in the reconstruction of multiple triple helix domains. The refolded collagen still had weak self-assembly ability and formed a unique network-like structure containing small interlaced and closely combined fibers, which shows favorable cell compatibility and potential applications.