Owing to the publicity and externality of watershed governance, collaborative governance among cities has become an inevitable choice to improve watershed governance performance and promote sustainable development of watersheds. Existing studies have provided many enlightenment on promoting watershed collaborative governance (WCG), while most of them investigated WCG from single or several dimensions with scanty quantitative empirical studies. Against this background, this study aims to establish a comprehensive WCG research framework involving multiple phases and diverse actors to empirically measure the synergy degree of WCG. Specifically, this study constructs a WCG index system composed of resource investment, open cooperation, and performance supervision subsystems that involves actors of government, enterprise, and the public. Using the complex system synergy model, an empirical analysis is performed to evaluate the synergy degree of Taihu Basin collaborative governance among and within cities in Jiangsu province, China during 2014–2020. The results reveal that the Tai Basin collaborative governance among cities was still in the run-in adaptation stage, which was primarily constrained by the discrete open cooperation subsystems among cities. The synergy degree of Taihu Basin collaborative governance within cities presented significant differences. Several targeted implications are proposed according to the results. This study provides a comprehensive index system for synergy degree measurement of WCG and could offer effective guidance for policymakers to design effective strategies for improving WCG performance.