Flower color is one of the most ornamental values of Meconopsis wilsonii, but very limited studies have been reported on its flower color formation. The UDP-glycosyltransferase (UGT) gene family plays a crucial role in plant flower color formation. In this study, the full-length transcriptome data of M. wilsonii was used to identify MwUGTs, focusing on protein physicochemical properties’ subcellular localization, and phylogenetic relationships. In addition, sequence analysis, expression pattern analysis, subcellular localization, and functional validation of MwUGT2 were also performed. A total of 26 MwUGTs were identified in full-length transcriptome and clustered into eight subgroups. Phylogenetic analysis and KEGG database annotation showed that MwUGT2 is associated with anthocyanin synthesis and accumulation. Subsequently, based on the expression of MwUGT2 during flower development and in different tissues, it was preliminarily determined that MwUGT2 plays a role in the flower bud stage. Subcellular localization assays suggested that MwUGT2 is present in the nucleus and cytoplasm. Overexpression in Nicotiana tabacum showed that MwUGT2 significantly increased the content of Cyanidin-3-O-glucoside and resulted in dark pink flowers in transgenic plants. In summary, our findings suggest that MwUGT2 plays a crucial role in the biosynthesis of anthocyanin and will also contribute to understanding the mechanisms of flower color formation in M. wilsonii.