The present invention relates to the technical field of biomedicine, and specifically discloses a DNA hydrogel-based functional nucleic acid protective carrier, which is prepared by means of self-assembly of a degradable high-molecular polymer containing a DNA-modified side chain, a functional nucleic acid, and a cross-linking agent. Compared with the prior art, a DNA hydrogel of the present invention is capable of in-situ self-assembly in an aqueous solution at room temperature to form particles with controllable and uniform sizes; the particles have a good stability under physiological conditions, can significantly slow down the degradation of a nuclease on the functional nucleic acid coated inside the DNA hydrogel, and can effectively transport the functional nucleic acid into cytoplasm without using any transfection reagents such as cations and viruses. Therefore, a therapeutic effect is achieved, and the toxic and side effects caused by the introduced transfection reagents such as cations and viruses are avoided.