Scientific identification of ecological source areas is a fundamental step in establishing a regional ecological security pattern, and it holds significant importance in maintaining the stability of ecosystem service functions, protecting the integrity of current landscapes, and ensuring the health of urban residents. Inner Mongolia, as a key area for the construction of important ecological security barriers in the northern part of China, plays a crucial role in climate balance, water regulation, biodiversity maintenance, and soil and water conservation. In recent years, however, due to human activities, there has been a surge in ecological degradation in Inner Mongolia, affecting regional ecological security and sustainable development. Therefore, taking Inner Mongolia as an example, based on the evaluation of ecological carbon sequestration, habitat quality, water production services, and soil conservation services, a Zonation model is used to analyze the landscape nested sequences of high and low ecological importance, and to identify the ecological source areas of Inner Mongolia. The evaluation results indicated that while all four types of ecosystem services are distributed from high in the east to low in the west, there are notable variations in the central region. Moreover, the water yield and soil conservation services in this region are comparatively lower. The model analysis revealed that the total area of ecological source areas in Inner Mongolia was 353032.4 km2, with primary ecological source areas covering 118040.3 km2, mainly distributed in regions such as the Hulunbuir Plateau and the southern part of the Greater Khingan Mountains. Secondary and tertiary ecological source areas are distributed along the periphery of the first and Secondary areas in sequence. The overlay analysis of ecological source areas and ecological redlines showed that there are 157444.9 km2 of ecological source area within the existing ecological redlines currently, accounting for 44.6% of the total ecological redline area. In the future, it is necessary to consider how to integrate the priority identification results of ecological source area protection with the existing ecological protection redlines. This should be accompanied by a classification system based on the actual situation of the region, and the formulation of management rules and strategies at different levels to promote more efficient implementation of regional ecological security protection. This study can lay the foundation for the rational construction of the ecological security pattern in Inner Mongolia and other arid regions, and provide strategies and suggestions to assist in the sustainable development of national spatial ecology.