Basin governance is an important issue in the modernization of national governance capacity and system. In the context of climate change, basin governance faces many challenges such as deep uncertainty, value pluralism and institutional complexity, and the traditional basin governance model of “certainty seeking” is facing increasingly significant theoretical limitations and practical limits. The emergence and development of “wicked” theory provides useful insights for basin governance under deep uncertainty. Based on the perspective of “wicked” theory, we analyze the scientific cognitive dilemma, collaborative governance dilemma and institutional design dilemma faced by watershed governance, and propose countermeasures to transform the watershed governance model from the perspective of “cognitive-method-technical-mechanical” four-dimensional synergy. In the cognitive level, the scientific understanding of climate change impacts on watersheds should be improved; in the methodological level, the transition from incremental adaptation to transformative adaptation should be promoted; in the technical level, the application of technologies for deep uncertainty should be promoted; and in the mechanism level, the construction of a basin governance structure centered on the basin community should be accelerated, so as to promote the transformation of basin governance model and the modernization of governance capacity.