The present invention provides a method for extracting medical material-based collagen from fish scales. The method comprises: (1) washing fish scales: using a decolorizing agent and hydrogen peroxide to decolorize the fish scales, and washing the decolorized fish scales; (2) placing the fish scales in an ethylenediaminetetraacetic acid solution, stirring, changing the ethylenediaminetetraacetic acid solution every 10-15 h, and draining the water; (3) carrying out stirring washing on the fish scales; (4) placing the fish scales into an acetic acid solution, adding protease to carry out enzymolysis gel extraction, centrifugating, and taking the supernatant; (5) adding the supernatant to a saturated NaCl or (NH4)2SO4 solution, standing, centrifugating, taking the precipitated crude collagen, and carrying out dialysis purification; and (6) carrying out freezing drying. According to the present invention, with the prepared collagen, the nature structure of the collagen can be well maintained; the fish scales are subjected to the decolorizing pre-treatment, such that the melanin on the surface of the fish scales is removed, and the color of the collagen is improved; the collagen purity is improved; and with the enzymolysis collagen extraction, the collagen yield is improved.