The increasing prevalence of cross-domain public affairs presents new challenges to government structures and governance capacity. In this context, building cross-domain intergovernmental cooperation has become essential for addressing public issues like river basin governance. While existing research has mainly focused on intergovernmental cooperation in watersheds of humid areas, studies on watershed management in arid regions remain scarce. To address this gap, this study examines the cooperative network in river basin governance formed by the government and local governments of Xinjiang Uygur Autonomous Region, China in the Kashgar River Basin. Using social network analysis, we explore the evolution, structure, and internal dynamics of this cooperative network, analyzing the forms, characteristics, and results of intergovernmental cooperation in river basin governance. Data was collected from the regulations and policies on Kashgar River Basin governance published by the official websites of the Xinjiang Uygur Autonomous Region government and local governments, focusing on intergovernmental cooperation documents for the social network analysis. The findings reveal the following: (1) The Kashgar River Basin governance has developed a stable, multi-agent intergovernmental cooperation network. River basin governance is increasingly characterized by multi-coordination, with deepening cooperation among water-related departments and the inclusion of ecological and other related departments. (2) The governance structure of the Kashgar River Basin follows a “core-periphery” model, where river basin management institutions and water conservancy departments hold core positions, driving multisectoral coordinated actions through horizontal collaboration. (3) Vertical power dynamics shape the intergovernmental cooperation structure, encouraging local governments in the basin to overcome institutional inertia and departmental silos, fostering effective cross-sectoral cooperation. This study offers valuable insights for optimizing intergovernmental governance structures in river basins and exploring ways to achieve regional win-win outcomes in river basin management in arid regions.