Tarocco is a prevalent blood-orange variety in China, has a bud variant identified in Wenzhou City. To characterize the quality traits and molecular mechanisms underlying inhibition of anthocyanin synthesis in this variety, we collected fruits of Tarocco (WT) and the bud variant Ouya (MT) at nine developmental stages. Their anthocyanin, soluble sugar, and organic acid profiles were examined, and transcriptomes and metabolites were analyzed at three developmental stages. The results revealed that MT is a new blood orange variety with weak anthocyanins and a better sugar-acid ratio than the WT. The content of anthocyanin in MT fruits were significantly lower than those in WT fruits, especially cyanidin-like anthocyanins, while the flavone contents exhibited no remarkable variation. A total of 64 differentially expressed genes (DEGs), including five transcription factors (TFs), five methylation-related genes, and one flavonoid biosynthesis gene, were identified between WT and MT at three fruit developmental stages. The potential regulatory networks of these TFs were further constructed using weighted gene co-expression network analysis.Furthermore, in MT fruit treated with the 5-azacytidine, we observed hypomethylation of anthocyanins accumulated in the pulp and the promoters and genebodies of some anthocyanin synthesis-related genes. These results provide new insights into the influence of DNA methylation on anthocyanin accumulation in MT and also provide support for the promotion of MT as a new variety.