As many manufacturing cities are currently experiencing serious environmental deterioration and energy crises, it is essential that they implement sustainable transitions by using cleaner production (CP) as a hopeful tool. We summarized the CP instruments applied in manufacturing cities and investigated their effect in urban sustainable transitions in this paper, by selecting Dongguan-a typical manufacturing hub in China-as a case. 264 related documents of policies, regulations, files, and notices promulgated by the Dongguan government during 2002–2017 were analyzed via content analysis to reveal the priority of major utilized tools for policy makers. We also summarized and analyzed the lifespan, dynamic trajectory, performance, function, and quantitative outcome of integrated CP instruments for sustainable transitions. It was found that CP instruments effectively decrease pollution generation, save energy, reduce resource consumption, and adjust and optimize industrial structure. It was also revealed that CP instruments embedded in sustainable transitions strategies was more effective and efficient at urban scale than that at larger scale. This paper provides a general reference for integrating CP instruments to push forward sustainable transitions in manufacturing cities, especially those cities without local legislative power in developing countries.