To improve the bioavailability of paprika oleoresin (PO), this study applied microencapsulation technology and evaluated its effects on yolk pigmentation, yolk lipid composition, and hepatic metabolic function in laying hens. Integrated transcriptomic and metabolomic analyses were used to explore the underlying molecular mechanisms. Laying hens were assigned to a control group (CK), a conventional PO group (F, 30 mg/kg), and microencapsulated paprika oleoresin (MPO) supplementation groups (P1–P4: 15, 30, 45, 60 mg/kg). After a 2-week adaptation period, the hens were fed the experimental diets for 8 weeks. The P1 group exhibited a 33% increase in yolk redness (a* value) compared with the F group (P < 0.05). Compared with the CK group, yolk lecithin content increased by 9.01% in the F group and 12.14% in the P2 group, while hepatic superoxide dismutase (SOD) activity was significantly elevated and malondialdehyde (MDA) levels were significantly reduced (P < 0.05). Integrated multi-omics analysis suggests that MPO is associated with remodeling changes in the hepatic metabolic network through the “amino acid–TCA cycle–oxidative phosphorylation” axis, which may enhance methyl donor and carbon skeleton availability for lecithin synthesis. This study suggests that microencapsulation can enhance PO deposition in egg yolk, improve hepatic metabolic homeostasis, and increase yolk lecithin content, supporting the development of natural and efficient functional feed additives.
