From the characteristics of military engineering construction which are different from civil engineering construction, this paper brings forth the background of the harmonious management of military engineering construction. Based on organizational behavior, military engineering economics, system coevolution, and from the point of ontology, epistemology and methodology, this paper describes the logical relationship and system framework of the “persons events things”, and operation mechanism of the harmonious management of military engineering construction, then builds up the theoretical framework of the harmonious management of military engineering construction. From the point of the Renli harmony of “leaders employees group” subject factors, Wuli harmony of “quality construction period cost” object factors, Shili harmony of “knowledge tool method” relationship factors, system environment harmony of “military technology economy”, this paper discusses the realization mode of the harmonious management of military engineering construction, then sets up the evaluation model of the harmonious management mode of military engineering construction.