Water environment quality is profoundly driven by a series of landscape characteristics. However, current knowledge is limited to the independent response of water quality to single landscape elements; this has led to poor knowledge of the potential role of structural coupling within landscapes in driving water quality changes, especially in those agroforestry-mixed mountainous watersheds with highly embedded forest-clustered landscapes and abundant headstreams. Given this fact, this study aims to evaluate whether and how the source–sink coupling structure of forest-clustered landscapes systematically drives headstream quality dynamics. We first systematically assessed the association pattern of source and sink structures within forest-clustered landscapes, and then innovatively proposed and constructed a functional framework of source–sink coupling structure of landscapes across 112 agroforestry-mixed mountainous sub-watersheds in Chongqing, China. On this basis, we further evaluated the driving pattern and predictive performance of the source–sink coupling structure of landscapes behind headstream quality dynamics. We report three findings: (1) headstream quality varied across agroforestry-mixed sub-watersheds, mapping out the source–sink structures and functions of landscapes; (2) there was significant functional coordination between source–sink structures of the forest-clustered landscapes, which significantly drove headstream quality dynamics; (3) the structural positioning and differences of the forest-clustered landscapes along the multivariate functional axes directly corresponded to and predicted headstream quality status. These findings together highlight a key logic that the response of water quality dynamics to landscapes is essentially that to the functional coupling between the source–sink structures of landscapes, rather than the simple combination of a single landscape contribution. This is the first study on the landscape–runoff association from the perspective of source–sink structural coupling, which helps to deepen understanding of the correlation mechanism between water dynamics and landscape systems, and provides a new functional dimension to the development of future landscape ecological management strategies from a local to a global scale.