The invention relates to the technical field of fruit processing and specifically relates to a method for separating pulp from seeds of a dragon fruit based on a biological enzyme process. The method comprises the following steps: 1) breaking the pulp of a dragon fruit to obtain dragon fruit paste; 2) adding a color protection agent into the paste obtained in the step 1) for color protection treatment; 3) adding pectinase and/or cellulase into the dragon fruit paste after the color protection for enzymolysis; 4) performing centrifugal separation of the dragon fruit paste treated in the step 3), and filtering to obtain dragon fruit seeds and juice. According to the method, quick enzymolysis is realized on the components such as pectin and fiber not good for seed fetching in the dragon fruit pulp through a pectinase or cellulase enzymolysis way, thus viscosity between the pulp and the seeds is reduced, the juice rate is increased, and separation is facilitated; the method avoids damage of the seeds; the obtained seeds and juice can be added into other food production.