Cyanidin-3-glucoside (C3G) has been found to prevent/treat intestinal disease and maintain gut homeostasis. Numerous studies have proved that nanoliposomes can improve the absorption and utilization of food nutrients. However, the impacts of C3G nanoliposomes (C3G-NL) are still unkown. This study investigated the effects of cyanidin-3-glucoside nanoliposomes (C3G-NL) on intestinal inflammation and permeability using a Caco-2/RAW264.7 co-culture model. ELISA and qPCR results showed that C3G-NL reduced pro-inflammatory markers, including TNF-α, IL-6, IL-8, cyclooxygenase-2, and inducible nitric oxide synthase, while inhibiting the NF-κB/MAPK pathway. C3G-NL also improved intestinal barrier integrity by increasing transepithelial electrical resistance and upregulating tight junction proteins (zonula occludens-1, occludin, claudin-1). Additionally, C3G-NL enhanced C3G metabolism, leading to the formation of intermediary metabolites like chalcone and dihydroflavonols, which contributed to the synthesis of other anthocyanins (delphinidin, peonidin, petunidin, malvidin, and pelargonidin). Overall, C3G-NL helps mitigate inflammation and restore tight junction integrity via metabolic regulation.