Objective In order to better grasp the Helan Mountain (Mts. Helan Shan region) Nature Reserve of small mammal animal population pattern and fauna distribution, and provide scientific basis for mice and rats transmit disease prevention of forestry department and the tourism, also provide the basic data for the study of biology of small mammals. Methods In 2012 October-2013 October on the activity peak in Helan Mountain donglu Gunzhongkou and Suyukou two region of 4 forest belt, acquisition of small mammal specimens, combined with the comprehensive arrangement of previous literature, a small mammal animal population distribution information data in the database, using Excel 2003 and animal community similarity analysis. Results The nature reserve has a total of 43 species of small mammals, belonging to 6 orders, 10 families and 32 genera. Analysis shows that, Rodentia, Cricetidae, Muridae and jerboa total 26 species, is the fundamental group of small mammals area of Helan Mountain Nature Reserve, North bellied rat (Niviventer confucianus) is the predominant species. In 43 species of small mammals in Helan mountain in the animal, 30 species of Palaearctic region, 12 species of Oriental realm, wide cloth 1. Conclusion Through the investigation, we mastered the population structure and distribution of small mammals animal in some areas in Helan Mountain Natural Reserve, but also provide the basis for further research on this area in infectious diseases.