The invention provides a method for preparing a biological scaffold by 3D printing. The method comprises the steps of grinding allogeneic bones or heterogeneous bones at a low temperature in a freezing grinder to obtain a printing material, modeling 3D printing with the aid of a computer, and then performing post treatment in a genipin solution. The prepared biological scaffold has good biological compatibility, and the bone graft material does not have toxicity, rejection, mutagenicity or antigenicity in vivo, and does not disturb bone and tissue regeneration; the prepared biological scaffold can be gradually degraded and absorbed and replaced by autologous bone tissues, can bear the pressure close to 20MPa with normal bone cortex, and has good initial mechanical properties; and the elastic modulus is gradually reduced, stress shielding is avoided, fracture, collapse and loosening of implants in the long-term healing process are avoided, bone fusion can be accelerated, and the implants can be finally completely converted into autologous bone tissues.