Obesity and associated metabolic conditions have emerged as significant public health issues impacting a considerable portion of the world’s population. An effective strategy for addressing obesity and related metabolic conditions involves promoting the browning phenomenon of white adipose tissue (WAT). Naturally occurring polyphenol hydroxy flavonoid myricitrin (MYR) possesses a wide array of physiological and pharmacological functions. However, the effect of MYR on regulating beige browning was not yet investigated. This study investigated the function of MYR in activating browning phenomena in the WAT of mice through the estrogen receptor alpha (ERα) pathway. Our results revealed that MYR treatment induced thermogenesis and browning in C3H10T1/2 adipocytes, and sequencing analysis and western blotting detection further indicated that ERα signaling pathway was significantly activated by MYR. The MYR supplementation also promote beige browning partly by activating the ERα-peroxisome proliferator-activated receptor gamma coactivator 1-alpha (PGC1α)-uncoupling protein 1 (UCP1) signaling pathway in mice. Furthermore, MYR treatment markedly suppressed body weight gain and enhanced energy expenditure in obese mice subjected to a high-fat diet. Overall, these results imply that MYR treatment may mitigate obesity by promoting the ERα pathway-mediated activation of the browning mechanism in mice’s inguinal WAT (iWAT). By improving beige fat thermogenesis and browning, our study thereby offered a potential natural compound to mitigate obesity and related metabolic complications.