The management of healthcare security fund involves multiple functional departments of the local government, and each department undertakes corresponding responsibilities. It is essential to build a cross-departmental collaborative management mechanism for the fund. Learning from the relevant policies and regulations of central and local healthcare security, the institutional framework for the cross-departmental collaborative management of local medical security funds is constructed from four aspects of organizational coordination, fundraising management, operation management, and use supervision And takes Zhejiang, Shanxi and Heilongjiang Province as examples to summarize the local practice. Based on this, the paper proposes a practical path to improve the cross-departmental collaborative management which includes clarifying the responsibilities of collaborative departments in the form of laws and regulations, improving the organizational guarantee of the inter-departmental collaboration mechanism, establishing a big data information system, and strengthening cross-departmental collaboration and management capacity.