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Introduction: China’s organised health system has remained outdated for decades. Current health systems in many less market-oriented countries still adhere to traditional administrative-based directives and linear planning. Furthermore, they neglect the responsiveness and feedback of institutions and professionals, which often results in reform failure in integrated care. Complex adaptive system theory (CAS) provides a new perspective and methodology for analysing the health system and policy implementation. Methods: We observed the typical case of Qianjiang’s Integrated Health Organization Reform (IHO) for 2 years to analyse integrated care reforms using CAS theory. Via questionnaires and interviews, we observed 32 medical institutions and 344 professionals. We compared their cooperative behaviours from both organisational and inter-professional levels between 2013 and 2015, and further investigated potential reasons for why medical institutions and professionals did not form an effective IHO. We discovered how interested parties in the policy implementation process influenced reform outcome, and by theoretical induction, proposed a new semi-organised system and corresponding policy analysis flowchart that potentially suits the actual realisation of CAS. Results: The reform did not achieve its desired effect. The Qianjiang IHO was loosely integrated rather than closely integrated, and the cooperation levels between organisations and professionals were low. This disappointing result was due to low mutual trust among IHO members, with the main contributing factors being insufficient financial incentives and the lack of a common vision. Discussion and Conclusions: The traditional 'organised health system' is old-fashioned. Rather than being completely organised or adaptive, the health system is currently more similar to a s'emi-organised system'. Medical institutions and professionals operate in a middle ground between complete adherence to administrative orders from state-run health systems and completely adapting to the market. Thus, decision-making, implementation and analysis of health policies should also be updated according to this current standing. The simplest way to manage this 'new system' is to abandon linear top-down orders and patiently wait for an explicit picture of IHO mechanisms to be revealed after complete and spontaneous negotiation between IHO allies is reached. In the meantime, bottom-up feedback from members should be paid attention to, and common benefits and fluid information flow should be prioritised in building a successful IHO.