To explore the effect of glutaraldehyde (GA) and 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide (EDC) cross-linking on the biophysical and chemical properties of acellular scaffold to better provide suitable donor materials for tendon reconstruction. GA and EDC with different concentrations and action time gradients were used to cross-link the acellular scaffold. By detecting the collagen content in the cross-linked scaffold and the cytotoxicity, the cross-linking scheme with minimal damage to the scaffold and minimal cytotoxicity was explored for subsequent studies. The biomechanical properties (durability, elastic modulus, stressmax) of the scaffolds in GA, EDC, acellular scaffold, and tendon groups were compared, and the scaffold rat models were constructed to further evaluate their in vivo histocompatibility. Under different concentration gradients, the collagen content of the scaffolds in the GA and EDC groups had no obvious difference. When 0.5% GA was cross-linked for 24 h, and the mass ratio of EDC (1:2) was cross-linked for 4 h, the inhibition rate of the scaffold extract on fibroblasts was the lowest. In the mechanical property test, the Stressmax, durability, and elastic modulus of the cross-linked acellular scaffolds were significantly improved than those before cross-linking, and the elastic modulus of the EDC acellular scaffold was similar to that of the bovine tendon. In the compatibility test, compared with the acellular scaffold group, fibroblast activity in the GA group decreased obviously, and the scaffold implanted in rat models led to a persistent chronic inflammatory reaction. However, cells in the EDC group could maintain good activity. Moreover, the scaffold had good compatibility with rats and did not cause an obvious inflammatory reaction. EDC cross-linking scheme will not damage the acellular scaffold, and the cytotoxicity of the obtained scaffold is controllable. Additionally, EDC cross-linked acellular scaffold has mechanical properties similar to normal tendons and excellent histocompatibility.