Poverty remains a significant global challenge, particularly in severely impoverished areas where balancing eco-civilization and economic growth is crucial. This study aims to analyze livelihood assets, determine appropriate strategies, and establish an eco-compensation model based on ecological vulnerability in Longnan City. We developed a livelihood evaluation index system using the Sustainable Livelihoods Framework and entropy weight method to assess the vulnerable portfolio of livelihood assets. We examined poverty causes and proposed targeted alleviation measures. Additionally, we created an “Eco-Compensation Model of Longnan City” incorporating the Sloping Land Conversion Program, key industries exit compensation, and cross-provincial water compensation based on incentive and punitive mechanisms. Our findings reveal that severely impoverished areas in Longnan City are primarily in the central, southern, and northwestern regions. Poverty is driven by unfavorable natural conditions, frequent natural disasters, regional economic marginalization, inadequate infrastructure, and a limited agricultural structure. The evaluation shows that natural capital in the five areas is lower than the national average level. We propose targeted measures for different vulnerable livelihood portfolios. The eco-compensation model provides a scientifically calculated compensation standard, offering a crucial funding source for implementing targeted poverty alleviation strategies.