Tissue engineering techniques aim to improve or replace biological tissues or organs by utilizing the extracellular matrix to facilitate the repair of damaged tissues or organs. Collagen-based scaffolds offer numerous advantages, including excellent biocompatibility, low immunogenicity, biodegradability, hemostatic properties, and mechanical strength. Collagen scaffolds can reconstruct the extracellular microenvironment, promote cell adhesion, migration, proliferation, and differentiation, and play a critical role in cell-to-cell and cell-to-matrix interactions. Collagen has been extensively utilized in tissue engineering to facilitate tissue repair and organ reconstruction. This review examines the properties of collagen, including its composition, structure, biological characteristics, and role in regulating various cellular behaviors. Additionally, the preparation of cell-loaded collagen scaffolds is discussed, along with a comprehensive overview of their applications in various tissues, including skin, nerve, bone/cartilage, heart, liver, and others. Emerging strategies and future perspectives for clinical tissue repair are also presented. This review provides a comprehensive synthesis of the mechanisms underlying the use of cell-loaded collagen scaffolds as advanced biomaterials, emphasizing their potential to expand the clinical applications of collagen.