The cost control of engineering project is not decided by single factor. If we want to control the cost systematically, we should deal with the relationship between each factor comprehensively to reach the balanced state. Total Factor Management includes project duration, quality, risk, scope, procurement, health, safety and environment. Total Factor Cost Management of engineering project is to quantify such factors as quality, duration and cost on the premise that they are related and constrained each other, then, establish the relationship and coordinate the management with the cost factors. Therefore, the method of integrated cost management came into being, which is an effective method for the integrated management of various factors, because the project cost and quality, duration are directly related to each other, the speed and quality of the project duration are closely related to the project cost. Therefore, the project cost management, should be at the same time cost, schedule, quality of these three basic elements of comprehensive integrated management. Therefore, by combining the theory of total factor cost management with the method of cost integrated management, the research train of thought of total factor cost integrated management based on three major factors in the cost control and construction stage of engineering project is determined, has shaped the innovative cost management model.