The Supplementary Provisions to the Social Insurance Fund Accounting System (hereinafter referred to as the Supplementary Provisions), issued by the Ministry of Finance, supplements and refines the original accounting system regarding businesses administered by healthcare security administrations, including long-term care insurance (uniformly administered by healthcare security administrations), premiums collected for future years of rural residents’ basic medical insurance, and advance payments for the centralized volume-based procurement of pharmaceuticals and consumables. Grounding its analysis in the financial management practices of healthcare security agencies, this paper systematically interprets the core content and key accounting points of the Supplementary Provisions, analyzes critical operational links and common difficulties in practice, and further proposes implementable suggestions for smooth implementation from three dimensions: organizational collaboration, business processes, and information systems, aiming to provide practical references for healthcare security administrations at all levels to ensure a stable transition to the new system.