The Yan Mountain Region (YMR), a transition zone between the Mongolian Plateau and northern China, played a pivotal yet understudied role in shaping the prehistoric East Asian genetic and cultural landscapes. Analyzing 42 ancient genomes (7700–4300 before present (BP)), focusing on the Early Neolithic Sitaimengguying (STM_EN) and Late Neolithic Jiangjialiang (JJL_LN) sites, we reveal the fine-scaled population history of the Neolithic YMR. We genetically link Early Neolithic YMR groups (Yumin and STM_EN) to the Early Neolithic Lake Baikal groups, in line with similar burial practices in the Lake Baikal region. JJL_LN individuals who belonged to the Late Neolithic Xiaoheyan culture were genetically heterogeneous reflecting an admixture between STM_EN-related groups and Yellow River farmers, and filled in an ancient genome sampling gap between the Hongshan and Lower Xiajiadian cultures. This study consolidates the idea of pre-pastoralist contact between the Eurasian steppe and northern Chinese agricultural societies and highlights the YMR as a key interaction sphere between the Yellow and West Liao River regions.