In order to set up an integrated greenhouse control system including environmental factors, plant growth period and upper index, relevant literatures of greenhouse control system were analyzed and based on control period principle, the literature was divided into three types of control systems: greenhouse environmental factors control system (fast speed time-varying systems), crop growing period control system (middle speed time-varying systems) and upper index control system in year (slow speed time-varying systems). By the multi-time-scale analysis, three types of control systems were found out to have multi-time-scale property. By means of singular perturbation theory, the greenhouse control system was designed hierarchically at first, and then the overall model of control system of greenhouse and the solution of the controller were obtained within such theoretical framework. Finally, the example and simulation results show that the proposed method is simple, effective and convenient for the application.