Cordycepin, a food-derived bioactive nucleoside from Cordyceps exhibits anti-aging properties, yet its mechanisms in Caenorhabditis elegans remain unclear. We demonstrate that cordycepin (0.1–0.5 mg/mL) extended lifespan by 10-12% under both normal and heat-stress conditions while improving multiple healthspan parameters without reproductive tradeoffs. Integrative analysis combining network pharmacology, multi-omics profiling, and genetic validation identified the insulin/IGF-1 signaling (IIS) pathway as a central mediator. Network pharmacology and molecular docking implicated an IIS-associated upstream node, with IGF-1R/DAF-2 emerging as a computationally prioritized candidate, while functional assays showed that cordycepin promotes DAF-16 nuclear enrichment and requires DAF-16 to extend lifespan. Transcriptomic analysis identified 3,755 differentially expressed genes (DEGs) enriched in FOXO signaling, autophagy, and stress response pathways, with Weighted correlation network analysis identifying 15 hub genes linked to longevity traits. Metabolomics detected 267 differentially expressed metabolites, highlighting enhanced glutathione-mediated antioxidant defense and remodeling of lipid metabolism centered on glycerol-3-phosphate, a membrane phospholipid precursor. Microbiome analysis showed selective enrichment of Bacillus spp. with positive lifespan correlation. Multi-omics integration revealed that cordycepin-mediated DAF-16 activation coordinates transcriptional reprogramming, metabolic homeostasis, and potential microbiome modulation through the conserved IIS/FOXO axis. This study supports cordycepin as a promising pro-longevity bioactive that functionally converges on evolutionarily conserved longevity pathways, while direct upstream target engagement remains to be established.