Seed germination and seedling emergence, incontrovertibly representing a critically essential and extremely vulnerable phase in the elaborate and ever changing plant life cycles, demonstrate an acutely high level of sensitivity to any minute and subtle alterations in environmental factors. Nevertheless, the effects of soil structural modifications on native plant seeds germination characteristics remain poorly understood, with the scarcity of comprehensive, detailed, and indepth quantitative observations available from field studies. This study examined the seeds of two representative native leguminous xerophytic shrubs (Lespedeza bicolor and Bauhinia brachycarpa) from dry valleys, quantifying germination processes, emergence rates, and seedling potentials across four rock fragment content (RFC) treatments (0%, 25%, 50%, and 75% v/v). The aim was to clarify the responsive patterns to changes in rock fragment content of soil and to explore the correlations nexus between seed germination characteristics and environmental factors. Results revealed significant impacts of soil rock fragment content variations on both shrub species' seed germination. Specifically, as the gradually increase of rock fragment content, both the emergence rates and seedling showed an upward trending pattern. Along the RFC gradient, Bauhinia brachycarpa seeds emergence rates showed a significant positive correlation with the mean topsoil temperature and the accumulated temperature, whereas Lespedeza bicolor seeds germination exhibited no significant correlations associated with temperature. Additionally, a significant negative correlation was found between soil water content and the germination abilities of both shrubs' seeds. Overall, medium to high levels of rock fragment content (50% and 75%) in the dry valley climate conditions led to an elevation in the topsoil temperature and a reduction in water content, which still promoted the germination of native shrub seeds. Moreover, it was also observed that Bauhinia brachycarpa seeds were more responsive to the changes in rock fragment content compared to Lespedeza bicolor seeds. These research findings substantially contribute to enhancing theoretical understanding of soil environment-seed germination interactions under drought conditions, providing valuable insights for ecological restoration and agricultural practices in stony mountainous regions.