The invention belongs to the field of microbial fungi, and relates to a Cordyceps militaris strain capable of producing heat-resistant proteinase and cordycepin at high yield and application thereof. The strain is prepared by the following steps: selecting a Cordyceps militaris wild-type strain newly separated from the natural world as the initial strain, carrying out composite mutagenization under the actions of Cordyceps militaris protoplast nitrosoguanidine and ultraviolet light, separating and screening to obtain the strain. The strain was collected by China General Microbiological Culture Collection Center on November 11th, 2016; the collection number is CGMCC No.13179; the strain is named HYCM12; and the classification designation is Cordyceps militaris. After the strain is subjected to deep liquid ventilation fermentation, the cordycepin content reaches 2.89 g/L, and the heat-resistant proteinase activity reaches 5326U/ml. Meanwhile, the method is simple to operate and easy to implement, has the advantages of short period, abundant and accessible raw material sources, low cost, no environmental pollution, low equipment and reagent price and the like, and is convenient for large-scale production.