Brown adipose tissue (BAT) is a critical target for obesity treatment, and exercise can enhance BAT function through the activation of ADRβ3. However, the molecular mechanisms underlying BAT metabolism following the exercise-induced activation of ADRβ3 remain unclear. This study utilized RNA sequencing, Western blotting, Oil Red O staining, weighted gene co-expression network analysis (WGCNA), and machine learning to investigate the role of the ADRβ3-COX2 pathway in lipid metabolism in brown adipocytes. We identified Ywhah as a key gene and validated our findings using external datasets. Our results demonstrate that exercise significantly enhances brown adipose tissue metabolism in mice, with ADRβ3 activation promoting metabolic activity in brown adipocytes. In contrast, COX2 inhibition notably reduced the lipolytic effect and thermogenic gene expression induced by ADRβ3 activation. WGCNA and machine learning identified Ywhah as the most important feature variable in the downstream signaling of the ADRβ3-COX2 pathway. External microarray data further confirmed that 8 weeks of aerobic exercise significantly upregulated Ywhah expression. Additionally, Ywhah displayed strong binding affinity to cytoskeletal proteins in affinity purification–mass spectrometry experiments, and its expression was highly correlated with cytoskeletal GSVA scores. In summary, this study reveals the potential role of the ADRβ3-COX2-Ywhah-cytoskeleton axis in regulating brown adipocyte metabolism, providing new insights into obesity treatment mechanisms.