Traditional Chinese medicine (TCM), a holistic medical system rooted in dialectical theories and natural product-based therapies, has served as a cornerstone of healthcare systems for millennia. While its empirical efficacy is widely recognized, the polypharmacological mechanisms stemming from its multi-component nature remain poorly characterized. The conventional trial-and-error approaches for bioactive compound screening from herbs raise sustainability concerns, including excessive resource consumption and suboptimal temporal efficiency. The integration of artificial intelligence (AI) and multi-omics technologies with network pharmacology (NP) has emerged as a transformative methodology aligned with TCM's inherent "multi-component, multi-target, multi-pathway" therapeutic characteristics. This convergent review provides a computational framework to decode complex bioactive compound-target-pathway networks through two synergistic strategies, (i) NP-driven dynamics interaction network modeling and (ii) AI-enhanced multi-omics data mining, thereby accelerating drug discovery and reducing experimental costs. Our analysis of 7288 publications systematically maps NP-AI-omics integration workflows for natural product screening. The proposed framework enables sustainable drug discovery through data-driven compound prioritization, systematic repurposing of herbal formulations via mechanism-based validation, and the development of evidence-based novel TCM prescriptions. This paradigm bridges empirical TCM knowledge with mechanism-driven precision medicine, offering a theoretical basis for reconciling traditional medicine with modern pharmaceutical innovation.