To address the heterogeneity in treatment effects (HTE) in precision medicine for coronary heart disease (CHD), we employed an individualized network analysis framework (Pheno-NM) to elucidate the molecular mechanisms of HTE in patients treated with Danhong injection (DHI). We integrated clinical phenotyping and transcriptomic data to identify three efficacy-based subgroups. The best-responding subgroup (D(+)S(+)) displayed the most complex gene network, with its key hub gene ORM1 linked to platelet activation. Individualized network analysis revealed that patient-specific symptom improvement correlated with unique functional module connectivity and gene expression variations (e.g., HSBP1L1 and KCNG2). Furthermore, six core network topological parameters significantly correlated with treatment efficacy and differed between subgroups (p < 0.05), alongside significant differential expression of genes such as IQCD and MTFR1. This work establishes a novel joint phenotype-genetic network modeling paradigm, providing a molecular framework for HTE and paving the way for precise, personalized cardiovascular interventions by revealing patient-specific network architectures.