The invention discloses a separation method for plant endophyte. The separation method comprises the steps of: sampling, surface sterilization, tissue grinding, separation and pure cultivation, and particularly comprises sampling health plants, storing in classification, soaking in an ethanol solution, soaking again in an sodium hypochlorite solution, washing by sterile water, weighing 0.3-0.3 g, adding the sterile water and grinding. The separation method further comprises the steps of: diluting the ground slurry in gradients, plate cultivating after coating, repeating each processing for 3-5 times, selecting single colonies according to eight phenotypic characteristics of bacterial colonies, consisting of shape, size, humidity, color, texture, surface, edge and transparency, for pure cultivation, and moving the pure cultivated single colonies into the test tube slants for preservation. Through the application of the separation method for plant endophyte, the diversity separation result of the plant endophyte is effectively prevented from being manually enlarged or lost; and the separation method for plant endophyte plays a very important role in researching the composition characteristics of plant endophyte colonies and enriching the gene resources of the endophyte.