Background <p>Plant-associated microorganisms significantly contribute to plant survival in diverse environments. However, limited information is available regarding the involvement of endophytes in responding to climate change and their potential to enhance host plants’ adaptation to future environmental shifts. <i>Pinus armandi</i>, endemic to China and widely distributed in climate-sensitive regions, serves as an ideal subject for investigating microbiome interactions that assist host plants in climate change response. Despite this, a comprehensive understanding of the diversity, community composition, and factors influencing endosperm endophytes in <i>P. armandi</i>, as well as the response of these endophytes to climate change, remains elusive.</p> Results <p>In this study, transcriptome data from 55 <i>P. armandi</i> samples from 13 populations were analyzed to evaluate the composition and diversity of active endosperm endophytes and predict their response to future climate change. The results revealed variations in community composition, phylogenetic diversity, and interaction network between the northern and southern groups. Temperature and precipitation correlated with endosperm endophytic species richness and diversity. Under projected future climate conditions, the northern group exhibits greater genomic vulnerability and anticipates increased threats, reflecting a corresponding trend in endosperm endophytes, particularly within the Ascomycota community.</p> Conclusion <p>The consistent threat trend from climate change impacting both hosts and endophytes emphasizes the potential importance of host-related fungi as crucial indicators for predicting future climate impacts. Meanwhile, this study establishes an initial framework for exploring host-microbial interactions within the context of climate warming and provides valuable insights for studies related to plant protection.</p>