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Structural control theory could be applied to study the control principles of social, economic and managerial systems. System Dynamics (SD) is the target field in social-economic sciences for endogenizing this theory, a subject that provides modeling solutions to real-world problems. SD models adopt diagrammatic representations, making it an ideal ground for transplanting structural control theory which utilizes similar graphic representations. This study sets up the theoretical ground for conducting structural control analysis (SCA) on SD models, summarized as a post-modeling workflow for SD practitioners, which serves as a specific application of the general structural control theory in social-economic sciences. Theoretical and practical establishments for SCA components are developed coordinately. Specifically, this study addresses the following questions: (1) How do SD models differ from physical control systems in graphic representations, and how do these differences affect the way of applying structural control theories to SD? (2) How could one identify control inputs in SD models, and how could different levels of system control in SD models be conceptualized? (3) What are the structural control properties for important SD components, and how could these properties and control principles help justify modeling heuristics in SD practice? (4) What are the procedures for conducting Structural Control Analysis (SCA) in SD models, and what are the implications of SCA results for model calibration and decision making? Overall, this study provides general insights for system control analysis of nonlinear dynamic simulation models, which may go beyond SD and extend to various disciplines in social-economic sciences.