The Ciliwung watershed is a national critical watershed which needs integrated management and restoration efforts. There are miscellaneous actors (government, private sector, and civil society), which create significant institutional complexity. To overcome this problem, a proper governance system to encourage an integrated approach to watershed ecosystems management and restoration (WEMR) is necessary. This research seeks to develop a proper multi-layered collaborative governance model for the Ciliwung WEMR using policy hierarchy theory and the life cycle of collaboration. This is a qualitative research and utilizes Soft Systems Methodology (SSM). Data were obtained through in-depth interviews, literature study, and focus group discussions. Research results illustrates how a multi-layered collaborative governance runs in the policy level, organizational level, and operational level. The result helps to reconstruct policy hierarchy theory, in which the authors developed interlinkages to connect all policy hierarchies. The model also needs quick wins and small wins as adjustments to a "good enough" governance approach. The research concludes that political work intervention in the Ciliwung WEMR is substantially important, in addition to the processes of technical-managerial works.