Under the environment of plateau alpine region, the new model of substitute construction separating government construction and management functions has gained great development in barracks construction, which significantly improves the risk management level of barracks facilities to some extent. From the significance of barracks facilities construction guarantee in highland alpine area, the article proposes a risk identification framework for the substitute construction unit of Someplace facilities in highland alpine area based on the whole life cycle of engineering projects. Combined with the risk identification framework, the risk evaluation index system of the agency construction unit is constructed, and then the AHP hierarchical analysis method is introduced to solve the weight of the indexes, and combined with the fuzzy comprehensive evaluation method, the AHP-FCM evaluation model is constructed. A barracks facilities project in a camp area is selected as a case study, and Company T is used as the research object to carry out data analysis of its risk degree using the AHPFCM model. In the construction of barracks facilities in highland and alpine areas, the biggest risk faced by the construction unit is the project implementation stage, the weight of which reaches 29.93%, and the fuzzy comprehensive evaluation of Company T’s risk score is 3.182, which is between medium and large risks. Therefore, the agency needs to examine and check its own risk factors in time, in order to lay a solid foundation for ensuring the smooth implementation of the agency project of barracks facilities in highland alpine areas.