Endoplasmic reticulum (ER) stress is known to impair the function of visceral adipose tissue (VAT) and subcutaneous adipose tissue (SAT), disrupting lipid metabolism. Despite the crucial role lipid plays in regulating adipose tissue function, the specific lipidomic alterations in VAT and SAT under ER stress remain unclear. In this study, ER stress was induced in VAT and SAT, and targeted lipidomic and transcriptomic approaches were used to analyze lipid metabolism and gene expression profiles. The results revealed that VAT exhibited a stronger ER stress response, characterized by a significant increase in binding immunoglobulin protein (BiP) expression and notable lipidomic disruptions, especially in glycerides and sterols. These disruptions were marked by a decrease in protective polyunsaturated fatty acyl species and the accumulation of lipotoxic molecules. In contrast, SAT displayed less severe lipidomic alterations. Transcriptomic analysis indicated that VAT was more susceptible to immune activation, inflammation, and metabolic dysfunction, while SAT primarily showed alterations in protein folding processes. These findings underscore the tissue-specific mechanisms of ER stress adaptation in VAT and SAT. In conclusion, VAT appears to be a critical target for addressing metabolic dysfunction in obesity and related disorders, with potential therapeutic implications for managing ER stress-induced metabolic diseases.