Abstract: Poria cocos, as a major traditional chinese medicinal material with an annual output exceeding tens of thousands of tons, boasts a substantial market scale. The "sweating" process of Poria cocos is a crucial post-harvest treatment step to enhance its quality. However, the current industry faces several challenges, including inconsistent product quality, extensive processing methods, and difficulties in controlling the "sweating" conditions, leading to low efficiency. To address these bottlenecks, this study innovatively investigates the fungal community structure and functional mechanisms during the "sweating" process of Poria cocos from a microbial perspective. By applying Illumina MiSeq high-throughput sequencing technology, key microbial taxa involved in this process were identified, and target strains were successfully isolated using pure culture techniques. For the first time, a functional strain labeled "YJ-001" (identified as Suhomyces ambrosiae) was discovered on the surface tissue of Poria cocos, which participates in the "sweating" process. Inoculation with strain "YJ-001" resulted in improved content of ethanol-soluble extracts, water-soluble polysaccharides, total polysaccharides, and total triterpenes in the "sweated" Poria cocos, while maintaining compliance with moisture and ash content standards. Notably, the levels of ethanol-soluble extracts, total polysaccharides, and water-soluble polysaccharides were significantly higher compared to those subjected to conventional "sweating". The findings indicate that strain YJ-001 enhances the effective components of Poria cocos through metabolic activities during the "sweating" process, thereby improving its quality. This research provides a new scientific basis for enhancing the quality and efficiency of the Poria cocos industry.