Abstract: Rapid urbanization, intensified agricultural production, and increasing human activities have exerted growing pressure on regional ecosystems, threatening ecological security and sustainable development in the Chengdu–Chongqing Twin-City Economic Circle. As an important strategic region for ecological protection and high-quality development in the upper Yangtze River Basin, identifying key ecological elements and revealing the evolution of ecological security patterns are essential for balancing agricultural production and ecological conservation. This study developed an integrated framework combining ecosystem service assessment, self-organizing map (SOM) clustering, morphological spatial pattern analysis (MSPA), circuit theory, and ecological network community detection to construct and optimize the regional ecological security pattern. Five ecosystem services, including habitat quality, water yield, carbon storage, soil retention, and net primary productivity, were selected to evaluate ecosystem service importance. The SOM algorithm was applied to identify ecosystem service bundle characteristics, and ecological sources were extracted by integrating high-value ecosystem service areas with MSPA. An integrated resistance surface was subsequently established by incorporating natural and socio-economic factors. Based on circuit theory, ecological corridors, ecological pinch points, and ecological barrier points were identified to characterize ecological connectivity and potential ecological bottlenecks. Furthermore, the Louvain community detection algorithm was used to reveal the spatial organization characteristics of the ecological network and identify ecological functional zones. Finally, the spatiotemporal evolution of the ecological security pattern in the Chengdu–Chongqing Twin-City Economic Circle from 2000 to 2023 was analyzed. The results showed that (1) Ecological sources exhibited an overall increasing trend from 2000 to 2023. The number of ecological sources increased from 34 to 76, and their total area expanded from 10,499 km² to 12,540 km². (2) Ecological connectivity was enhanced, with the number of ecological corridors increasing from 68 to 168 and their total length increasing from 8,570 km to 9,005 km. (3) Ecological pinch points increased from 1,062 to 1,688, with their area expanding from 1,365 km² to 1,965 km². Meanwhile, ecological barrier points increased from 40 to 68, and their area expanded from 941 km² to 1,712 km². (4) Eight ecological network communities were identified using the Louvain algorithm, and four ecological functional zones were delineated accordingly. Differentiated management strategies were proposed to promote coordinated development of agricultural production and ecological conservation. This study provides a systematic approach for optimizing ecological security patterns by integrating ecosystem services, landscape connectivity, and network community characteristics. The findings provide scientific support for ecological restoration, sustainable agricultural development, and ecological management in the Chengdu–Chongqing Twin-City Economic Circle