Eco-environmental zoning regulation, grounded in the “Three Lines and One List” framework, establishes a governance system that is comprehensive and process-oriented and integrates multi-stakeholder collaboration. As an integral ecological system, the Yellow River Basin must advance cross-regional collaborative governance while pursuing refined management within each control unit, a step essential to enhancing overall basin governance efficacy. Based on the PSR model, the SFIC model, and spatial governance theory, this paper constructs a four-dimensional “pressure-structure-process-space” analytical framework to systematically deconstruct the multidimensional drivers and interactive logics underpinning collaborative eco-environmental zoning regulation in the Yellow River Basin. Empirical analysis reveals that the pressure dimension creates an initial driving force through ecological carrying thresholds and rigid policy constraints; the structure dimension reshapes the governance network via institutional design; the process dimension fosters innovation in regulatory instruments through dynamic transmission chains; and the spatial dimension, acting as a contextual regulator, improves the alignment between geographical attributes and governance strategies. These four dimensions interact in a non-linear synergistic mechanism characterized by “pressure input-structural reconstruction-implementation feedback-spatial adaptation”. The multi-case comparative studies of collaborative eco-environmental zoning regulation practices across the upper, middle, and lower reaches, as well as the basin as a whole, identify three distinct collaboration models: an “ecological red-line + rigid institutional constraint” model in the upper reaches, a “resource constraint + policy-pressure driven” model in the middle reaches, and a “spatial optimization + digital-empowerment driven” model in the lower reaches. Overall, the basin should adopt a differentiated zoning regulation approach. To address existing challenges, optimization pathways should be pursued along two tracks: a universally applicable trajectory reflecting basin-wide regularities and a context-specific trajectory tailored to the unique conditions of various reaches.