This paper develops a new analysis framework to examine the complex interactions within a tobacco control system in relation to the effects of tobacco control instruments. To develop the framework, we critically review the current status of tobacco control, including what instruments have been put into place, how much these instruments are helping, what problems we still have, and the reasons for current problems. The framework presents the architecture of a tobacco control system and its dynamic cycle of policy making, enactment, monitoring and refinement for analyzing tobacco control issues. To help develop new effective tobacco control instruments, we propose a conceptual model and use smoke-free places as an example for illustrating the innovation process. The analysis framework and the conceptual model have the potential to help manage tobacco control policy innovation in the process of decision-making, decision-refinement and ongoing management of government activities.