Nature-based solutions (NbS) underscore a holistic approach centered around ecosystems to address challenges. Under the “carbon peaking and carbon neutrality "goal, the identification of core ecological carbon sequestration (ECS) areas within ecosystems lacks an effective grading model. Furthermore, the insufficient delineation of the relationship between carbon sink potential and economic development has impeded scientific planning and effective management. This study introduces an innovative hierarchical model for identifying ECS core areas, combined with an NbS framework. This study employs the InVEST-Zonation-MSPA modeling approach to construct the hierarchical model for ECS core areas. In the process of establishing the ecological security pattern (ESP), it measures the ECS advantage and employs the multiscale geographically weighted regression (MGWR) model to explain the spatial variations in economic responses to ECS advantage levels. The study considered Yunnan Province, which has rich ecological carbon sinks in the highland mountains of southwest China, as the study area. The key findings are: (1) The distribution pattern of priority levels for ecosystem services related to ECS shows a three-tiered pattern. Factors such as urban expansion and infrastructure development have reduced priority areas in ECS. (2) In the construction of the ESP, scenario A and scenario B identified 16.71 % and 14.64 % of priority areas as core ecological source areas, respectively. A linear relationship exists between minimum cumulative resistance (MCR) and the ECS advantage index (ECSAI). An equation was developed to explain 30.9 % of the variability in ECSAI, indicating that ECSAI increases to some extent with increasing MCR. (3) The hierarchical classification of ECS core areas is based on a priority protection area foundation formed jointly by ecological and carbon sequestration landscape priorities. Four levels of core areas (I, II, III, IV) are defined, representing 3.9 %, 6.2 %, 2.7 %, and 37.3 % of the total area respectively. (4) Economic factors exhibit significant spatial heterogeneity in their impact on ECS across counties. This study provides a quantitative analytical method for balancing carbon sequestration priorities with economic development. The results guide regional ecological conservation and carbon sequestration management.