[Objective] RNA-seq technology was used to sequence the larval guts of Apis cerana cerana under stress of Ascosphaera apis. Subsequently, trend was analyzed for differentially expressed genes (DEGs) to obtain significant gene expression patterns, followed by transcriptome analysis of A. apis stressing the larval gut.[Methods] Infected honeybee larval guts were sequenced at Illumina HiSeq 2500 platform and in-depth analyses were done using corresponding biological software. Finally, RT-qPCR was conducted to validate RNA-seq data.[Results] A total of 41133932 high-quality clean reads were obtained. Trend analysis result showed that 22865 DEGs were grouped into 8 gene expression patterns, among them 16769 DEGs were assigned to 4 significant expression patterns including 2 up-regulated trends and 2 down-regulated trends. GO enrichment analysis result showed that all DEGs within significant up-and down-regulated patterns were enriched in 40 and 37 GO terms, respectively, and the mostly enriched one is cellular process (2486 unigenes). KEGG enrichment analysis result displayed that the DEGs within significant up-and down-regulated trends were enriched in 119 and 112 pathways, respectively, and biosynthesis of amino acids (127 unigenes) and ribosome (98 unigenes) were mostly enriched. A. apis facilitated its proliferation through enhancing the biosynthesis and the host could fight A. apis by inhibiting the protein synthesis of the fungal pathogen during the stress process. Furthermore, expression levels of 11 DEGs enriched in the pathogen's MAPK signaling pathway decreased when the stressing time of A. apis was prolonged, suggesting that A. c. cerana larvae could constrain the pathogen's replication by disturbing this pathway.[Conclusion] This is the first report of transcriptome investigation of A. apis infecting A. c. cerana larvae. Our data provide gene expression profiles of A. apis stressing the larval gut of A. c. cerana, as well lay the foundation of unraveling molecular mechanisms regulating the pathogenesis of A. apis.