The invention discloses a method for separating deoxynucleotide from salmon seminal fluid, which comprises the following separation steps: S1, preparing fresh or frozen salmon seminal fluid tissue bodies, putting the tissue bodies into a glass homogenizer, adding a quantitative cell lysis buffer solution, homogenizing until no tissue clots exist, then transferring the tissue bodies into a centrifugal tube, adding protease K, uniformly mixing the tissue bodies and the protease K, and carrying out centrifugal separation; and S2, performing water bath in a constant-temperature water bath kettle for a fixed time, and intermittently oscillating the centrifugal tube for a plurality of times to preliminarily obtain mixed liquid. According to the method, the deoxynucleotide component in the salmon semen can be separated through the steps of oscillation, separation and the like by adopting a dissolution and centrifugal separation purification mode and adding quantitative protease K, a TE buffer solution, absolute ethyl alcohol and the like, so that the deoxynucleotide separated by the separation method is relatively high in purity and relatively high in purity. Compared with the traditional separation method, the method is simpler and clearer, is very convenient for personnel to operate, can efficiently and simply complete the separation work of deoxynucleotide, and has higher popularization value.