Background and Purpose: The presence of unique terpenes in Poria cocos (PC) enables it to treat various diseases. However, the modes of action (MOA) of PC have not been investigated. Hence, the present study was conducted to address this research gap via molecular docking and drug-induced transcriptome analyses. Experimental Approach: For molecular docking analysis, data on PC terpenes and druggable proteomes were collected from public databases. Transcriptome data generated using intestinal and brain cell lines were also collected. We compared the results of docking analysis and transcriptome analysis and constructed a diffusion network (DN) to bridge the gap between the results of the two analyses. The DN analysis was also proposed to confirm its MOA against Alzheimer’s disease (AD). Key Results: The docking and transcriptome analysis of PC allowed for the prediction of its existing clinical efficacy. Differences between the docking and the transcriptome analysis were also confirmed; however, the results of both analyses were complementary. Finally, the DN was constructed for AD, and the submodules of AD with which terpenes interacted were identified. The AD DN analysis confirmed the detailed pharmacological mechanism of PC. Conclusion and Implications: This study identified the MOA of PC using biological data and in silico methods. The method proposed herein can help identify the pharmacological MOA of complex natural products.