The invention discloses a method for performing bone and meat separation on fish wastes by utilizing microbial fermentation. The method comprises the following main steps: adding fresh fish wastes and water into a fermentation tank according to the mass ratio of 1:(1-3); introducing bacillus licheniformis HL-3 capable of producing high temperature-resistant proteases into the fermentation tank for fermentation; controlling the fermentation temperature to be 55-60 DEG C and the fermentation time to be 6-12 hours; after the end of fermentation, enabling materials in the fermentation tank to firstly pass through a large-aperture metal mesh screen for filtering and separation so as to obtain intercepted fish bones and then enabling the permeated materials to pass through a small-aperture metal mesh screen for filtering and separation so as to obtain intercepted fish meat. The method for performing the bone and meat separation on the fish wastes, disclosed by the invention, has the characteristics of being convenient and simple to operate and low in cost, thereby having a good application prospect.