Abstract: Under the combined impacts of strengthened ecological constraints, policy adjustments, and rapid urbanization, human–land relationships in natural heritage sites are undergoing profound restructuring. Assessing and mitigating farmers’ livelihood vulnerability has therefore become a key issue in balancing ecological conservation and regional development. Taking the Yancheng Yellow Sea World Natural Heritage Site as a case study, this study constructed a three-dimensional evaluation framework consisting of exposure, sensitivity, and adaptive capacity based on the Vulnerability Scoping Diagram (VSD) framework. The entropy weight method and obstacle degree model were employed to systematically identify the differentiation characteristics and key influencing factors of livelihood vulnerability among different types of farming households. The results showed that: 1) farmers mainly adopted proactive adaptation strategies, characterized by the optimization of planting and aquaculture structures and the diversification of livelihood activities, while passive adaptation behaviors were relatively limited; 2) overall livelihood vulnerability was low, but significant differences existed among household types, exhibiting a descending pattern of farming-dominated households, self-employed households, mixed-employment households, and wage-labor households. The livelihood vulnerability of farming-dominated households was nearly twice that of wage-labor households; 3) insufficient opportunities and capacity for occupational transition and low life satisfaction were the primary drivers of exposure and sensitivity, respectively, whereas the reduction of natural capital, inadequate household capital accumulation, and limited access to financial support constituted the main constraints on adaptive capacity. Overall, the formation of livelihood vulnerability exhibited a coupled transmission mechanism characterized by “livelihood type–capital endowment–differentiated response”. Accordingly, livelihood vulnerability mitigation should be promoted through the coordinated implementation of industrial development, capacity building, institutional support, and spatial optimization. This study provides micro-level empirical evidence for understanding the transformation of human–land relationships in protected areas and offers insights for developing differentiated livelihood governance strategies for farming households.