The coexistence of brown adipocytes with low and high thermogenic activity is a fundamental feature of brown adipose tissue (BAT) heterogeneity and plasticity. However, the mechanisms that govern thermogenic adipocyte heterogeneity and its significance in obesity and metabolic disease remain poorly understood. In the current study, we identified a population of JunB-enriched adipocytes (JunB+ adipocytes) within the brown fat depot that exhibits lower thermogenic capacity and smaller lipid droplets compared to high-thermogenic adipocytes. This population of JunB+ adipocytes exhibited marked expansion during obesity, in part through the induction of pro-inflammatory cytokines TNFα and IL-6. Depletion of JunB in adipocytes or UCP1+ adipocytes increased the fraction of adipocytes exhibiting high mitochondrial content and thermogenic capacity, leading to enhanced basal and cold-induced energy expenditure and protection against diet-induced obesity and insulin resistance. Mechanistically, JunB directly binds to the promoter of estrogen-related receptor α (Errα), a downstream effector of PGC1α, and suppresses its transcriptional function. JunB antagonizes the stimulatory effects of PGC1α-ERRα on mitochondrial biogenesis and high-thermogenic adipocyte formation. Taken together, our studies uncover a novel mechanism involving JunB that integrates metabolic and inflammatory signals and shapes the thermogenic adipocyte heterogeneity, serving a critical role in maintaining systemic metabolic health.