Peanut (Arachis hypogaea L.) is an important oil crop with economical interest. Peanut testa showed difference in colors, such as white, red, purple, pink and variegated. The molecular mechanism of the anthocyanin synthesis in variegated testa merit further in-depth research. In this study, the variegated testa peanut VG-02 was analyzed using Liquid chromatography tandem mass spectrometry (LC-MS/MS) analysis, in order to detect the relative changes in content of anthocyanins in variegated testa at different developmental stages. Twelve metabolites associating with the testa color were detected. In the comparison of F2-B2 at DAF45 (45 days after flowering and needling) stage the highest number of differential metabolites was revealed. The relative contents of cyanidin 3-O-galactoside and cyanidin O-syringic acid were lower by 0.63 and 2.35 fold in the pigmented area than that in the non-pigmented area, respectively. The relative contents of rosinidin O-hexoside, procyanidin A1, A2, B2, B3, cyanidin, delphinidin, delphinidin 3-O glucoside and cyanidin 3-O-galactoside were higher by 1.05 to 11.55 fold in the pigmented area than that in the non-pigmented area, respectively. Cyanidin and delphinidin were the main metabolites that caused the difference in color between the pigmented area and the non-pigmented area. RNA-seq analysis revealed 1,050 differentially-expressed genes (DEGs), which included 27 DEGs highly related to the synthesis of variegated testa color. Thirteen were up-regulated and 14 were down-regulated, including 3 PALs, 1 C4H, 2 CHSs, 1 F3H, 1 F3'H, 2 DFRs, 2 LARs, 2 IAAs, 4 bHLHs, and 9 MYBs. KEGG (Kyoto Encyclopedia of Genes and Genomes) enrichment analysis suggested that the metabolic pathways related to anthocyanin biosynthesis included phenylalanine metabolism, phenylpropanoid biosynthesis, flavone and flavonol biosynthesis, flavonoid biosynthesis, plant hormone signal transduction and circadian rhythm plant, among which flavonoid biosynthesis was proposed to be relevant with the testa variegation. Moreover, twenty DEGs were subjected for qPCR analysis. The similarity on transcriptional pattern revealed by qPCR and RNA-seq was observed. Collectively, the results of this study should help to further reveal the molecular regulatory mechanism of anthocyanin synthesis of the variegated testa in peanut.