The present invention discloses a preparation method for a chitosan-based porous scaffold with biological activity. According to the present invention, chitosan and inorganic micro/nanoparticles with biological activities are adopted as raw materials to prepare into slurry; a water-soluble aldehyde polysaccharide polymer is adopted as a cross-linking agent; a Schiff base cross-linking process and a freeze drying method are adopted to prepare a class of chitosan-based composite porous scaffold materials with biological activities, wherein porosities, pore sizes, mechanical properties, degradation performances, and bone conductions/bone inductions and the like can be regulated through the formula and the process conditions. According to the present invention, the porous scaffold provided by the present invention does not adopt harmful chemical cross-linking agents, and can not cause adverse effects to cells; with the cross-linked porous structure and a plurality of hydrophilic groups such as amino, carboxyl, hydroxyl and the like, the porous scaffold has high chemical stability in an aqueous phase with a wide pH range (pH range of 5-9), and has outstanding advantages of softness, high elasticity, swelling ratio of 30 times, and the like; the porous scaffold has advantages of imitation of natural bone extracellular microenvironment in aspects of the porous structure, the chemical composition, the surface chemistry and the like.