The invention relates to a method for extracting refined cordycepin from Cordyceps militaris fruit bodies. The technical scheme is that the method comprises the following steps of: crushing the Cordyceps militaris fruit bodies and passing through a 16-mesh sieve for future use; taking and soaking the crushed raw materials in ethanol with concentration being 70 percent and volume being three times of the volume of the raw materials for 24 hours; adding suspension obtained after soaking into a reflux device, heating and refluxing for 2-4 hours and filtering; extracting the filtrate for 2-5 times by using n-butyl alcohol; concentrating the supernatant liquid to alcohol-tasteless extract at 60 DEG C under reduced pressure; eluting the extract through a silica gel column, keeping the volume ratio of ethyl acetate to 95% ethanol of a mobile phase to be 5:3, recovering the eluent and conducting thin-layer chromatography (TLC) tracking and detection; distilling and concentrating the recovered eluent under reduced pressure to an extent that the volume of the concentrated eluent is one fifth of the volume of the received eluent; and crystallizing the concentrated eluent at room temperature. The method has the advantages that the amount of the used organic solvent can be reduced, the separation steps are reduced, the extraction rate is improved, the toxicity is reduced, the cordycepin in Cordyceps militaris can be enriched, the production cost is low and the purity of the cordycepin is higher.