With the increasing complexity of social public affairs, cross-departmental collaborative governance has become an important model of modern administrative management. However, conflicts of interest frequently occur during the collaboration process, which are mainly reflected in resource allocation, goal differences, and power games. These conflicts are caused by factors such as cultural differences within departments, inconsistent performance evaluation systems, and personal interests of department members. To address these issues, it is necessary to design multi-level integration mechanisms, including establishing stable communication channels and unified goals and evaluation systems. Successful integration cases in various fields, such as food safety supervision, environmental protection, and urban transportation governance, show that effective integration mechanisms need to establish institutionalized communication carriers, form a consensus target system, and design guarantee measures with both incentives and constraints. Although current research has achieved certain results, there are still limitations, such as insufficient attention to underdeveloped regions, a lack of consideration of cultural factors, and a narrow focus on internal government collaboration. Future research can explore differentiated integration models, introduce third-party assessment institutions, and strengthen research on the participation mechanism of enterprises and social organizations.