Endemic species are valuable models for understanding evolutionary processes and species adaptation in isolated environments. The Helan Shan pika (Ochotona argentata), endemic to a small region in the Helan Shan of China, represents a unique case of a species with a restricted distribution that is vulnerable to anthropogenic threats and rapid environmental changes. Despite its endangered status, genomic research on O. argentata remains limited. In this study, we present a high-quality genome assembly of O. argentata with high genome contiguity and gene-space completeness. The assembly reveals that 41.28% of the genome consists of repetitive sequences and a total of 24,374 annotated genes. We identified gene families that have undergone significant expansion or contraction, particularly those related to protein synthesis, metabolism, and other functions potentially linked to adaptation in high-altitude environments.. Genome synteny analysis revealed strong conservation between the O. argentata genome and the previously sequenced American pika (Ochotona princeps) genome, while also allowing us to characterize its sex chromosomes. Additionally, population demography analysis indicated a notable population decline in O. argentata approximately 300,000 to 500,000 years ago, coinciding with the mid-Pleistocene glacial period. Furthermore, we identified an increased genetic load in O. argentata compared to pika species with broader distribution ranges, indicating a consequence of inbreeding, likely driven by its highly restricted range and low genetic diversity. Our study provides the first comprehensive genomic resource for O. argentata, essential for understanding the evolutionary processes underlying endemism and conservation needs of the endangered Helan Shan pika.