The 2018 Party and state institutional reform established the Department of Veterans Affairs to centralize veteran management by integrating functions previously held by human resources and civil affairs agencies. However, a case study of the Veterans Affairs Bureau in L City reveals a stark contrast in implementation. While the new bureau successfully assumed preferential treatment duties from the Civil Affairs Bureau, it struggled to take over the resettlement of military transfer cadres from the Human Resources and Social Security Bureau. Adopting the Guikou Lingdao system framework, this paper examines the mechanisms driving this implementation paradox. The study finds that preferential treatment is a typical administrative function of the government, involving no Guikou supervision by Party functional departments. It aligns with the administrative integration logic of the reform plan, thus facilitating a smooth transfer. Conversely, the resettlement of military transfer cadres is deeply embedded in the Guikou Lingdao system chain of the “Organization Department—Human Resources and Social Security Bureau.” This creates a structural misalignment between the horizontal integration of administrative functions and the vertical concentration of existing Party leadership power. The study argues that administrative restructuring must align with the overarching Guikou Lingdao system; unless vertical Guikou relations are synchronized, the effectiveness of administrative integration will be significantly constrained.