<p>Research on carbon sequestration service ecological compensation is of great significance for achieving cross-regional green and equitable development, as well as the “carbon neutrality” goal. However, existing studies are mostly limited to static assessments, with room for improvement in the forward-looking analysis of carbon sequestration service ecological compensation patterns under future multi-scenario and multi-scale conditions. To this end, this study uses the Henan section of the Yellow River Basin as a case study, constructing an integrated analysis framework combining the PLUS model, InVEST model, and ecosystem service flow theory for “scenario simulation—carbon storage-based carbon sequestration value assessment - compensation priority identification.” Based on this framework, the study analyzes and simulates the carbon sequestration service compensation demand and spatial priorities under three scenarios (natural development scenario, economic priority scenario, and carbon sequestration service protection scenario) in 2030. The main findings of this study include: (1) The revealed mismatch between “stable total” and “dynamic priorities” in carbon sequestration service ecological compensation in the simulated scenarios: although the total compensation amounts at both city and county scales fluctuate by less than 1% across different scenarios, at the county scale, different development scenarios have a significant impact on compensation priorities, with the number of core compensation areas increasing from 2 in the natural development scenario to 7 in the economic priority scenario; (2) The preliminary proposal of a top-down, universal “tiered ecological compensation” policy framework. Based on the carbon sequestration service flow patterns revealed by the “city stability, county dynamic” simulations, it is suggested that higher-level financial compensation should focus on the long-term support of high-carbon sink functional areas, while lower-level government compensation should respond to the dynamic and precise allocation of compensation funds. This aims to achieve effective coordination between top-level design and grassroots implementation. This study not only fills the gap in the field of carbon sequestration service ecological compensation prediction but also provides new exploration and decision-making reference for the shift of regional ecological compensation policies from static assessments to dynamic adaptive planning.</p>