Collagen (Coll), as the basic material of matrix scaffolds for cell growth, has been widely used in the field of tissue engineering and regenerative medicine. In this study, collagen protein was modified by L-lysine (Lys), and cross-linked by genipin (GN) to prepare the L-lysine-modified collagen (Lys-Coll-GN) scaffolds. Microstructure, pore size, porosity, stability and biocompatibility of Lys-Coll-GN scaffolds were observed. The results showed that the bond between L-lysine and collagen protein molecule was formed by generating amide linkage, and mouse embryo fibroblasts proliferation was not inhibited in the Lys-Coll-GN scaffolds. In the multiple comparisons of Coll-scaffolds, Coll-GNscaffolds and Lys-Coll-GN-scaffolds, Coll-scaffolds was the worst in mechanical characteristics while the highest in biodegradation rate. Compared to Coll-GN scaffolds, Lys-Coll-GN scaffolds had more fiber structure, higher interval porosity (P<0.01). Although the tensile stress of Lys-Coll-GN scaffolds reduced significantly, its elongation length extended when the scaffolds was fractured (P<0.01). The percentage of Lys-Coll-GN scaffolds residual weight was lower than that of Coll-GN-scaffolds after all the scaffolds were treated by collagenase for 5 days (P<0.01).This study suggested that Lys-Coll-GN scaffold had good biocompatibility, and it improved the mechanical property and degradation velocity for collagen-based scaffold. This study gave a new predominant type of tissue engineering scaffold for the regenerative medicine.