Night shift workers face an increased risk of overweight and obesity due to circadian rhythm disruption, which can impair insulin sensitivity and promote fat accumulation and inflammation. Omics technologies, including transcriptomics, proteomics, metabolomics, and metagenomics, help identify the molecular mechanisms underlying these metabolic changes, including the roles of clock genes, hormones, and microorganisms. However, further human studies are needed, as much of the current evidence comes from animal models. This review examines omics-based research on circadian disruption and metabolic alterations associated with obesity risk in night shift workers, highlighting its potential to support personalized health interventions.