The presence of nanoplastics (NPs), which cause oxidative stress and damage to the cell structure due to the breakdown of microplastics (MPs), poses considerable ecological and health challenges. This study investigated the protective role of nobiletin (NOB), a flavonoid derived from citrus peel, in modulating autophagy and mitigating NP-induced toxicity in human intestinal Caco-2 cells. The Caco-2 cells were treated with NPs and varying concentrations of NOB to evaluate cell viability, apoptosis, and autophagic activity. We observed that exposure to NPs resulted in a concentration-dependent decrease in cell viability and an increase in the expression of apoptosis markers. Exposure to NPs reduced Caco-2 cell viability and disrupted autophagic processes by decreasing LC3B and increasing p62 levels, indicating impaired autophagy. NOB treatment reversed these effects by enhancing autophagic activity by upregulating LC3B and downregulating p62. Furthermore, NOB improved lysosomal integrity and decreased apoptotic markers such as Bax and cleaved caspase-3 while increasing Bcl-2 expression. NOB also facilitated the nuclear translocation of transcription factor EB through activating AMP-activated protein kinase (AMPK) and inhibiting mechanistic target of rapamycin (mTOR), promoting cellular detoxification and homeostasis. NOB has the potential as a therapeutic agent that leverages the autophagic pathway to mitigate the adverse effects of NPs, suggesting a novel approach for managing NPs toxicity in human intestinal Caco-2 cells.