Laying hens in the late laying period often experience reduced productivity and declining egg and meat quality, which limits breeding efficiency and resource utilization. This study aimed to evaluate the effects of multi-component Botanical Crude Extracts (BCEs) on egg and meat quality, metabolic health, and gut microbiota in aged laying hens. A total of 4320 hens were supplemented with 0.3% BCEs for 100 days, with evaluations at 60 and 100 days. BCE supplementation significantly enhanced egg flavor by promoting aromatic and fat-soluble volatiles and reducing odorous compounds (p < 0.05). BCEs improved yolk nutrition by enriching n-3 polyunsaturated fatty acids, especially docosahexaenoic acid (DHA), and optimizing the n-6/n-3 ratio (p < 0.05). A moderate reduction in amino acids was observed, which may reduce bitterness and ammonia burden (0.05 ≤ p < 0.10, trend). In muscle, BCEs improved protein–fat distribution, increased intramuscular fat, and enhanced flavor-related metabolites, significantly improving meat quality of culled hens (p < 0.05). BCEs also reshaped gut microbiota, reducing harmful taxa and promoting short-chain fatty acid and aromatic metabolite biosynthesis (p < 0.05). Serum metabolomics revealed modulation of AMPK, calcium, and cholesterol pathways, improving antioxidant capacity and lipid regulation (p < 0.05). Correlation analyses linked beneficial bacteria and metabolites with yolk DHA levels and flavor (p < 0.05). Overall, BCEs enhanced egg and meat quality and physiological health, providing guidance for functional feed strategies in aged laying hens.