Soybean (Glycine max L.) is an important economic crop, flavonoids (such as anthocyanins) and some other nutrients of which were significantly promoted after germination. The accumulation of anthocyanin is influenced by many kinds of factors in plants, the regulatory mechanism of which is relatively complex. Here, soybean double mutant stf1/2 was utilized and found that GmSTF1/2 participated in light-mediated anthocyanin production in soybean. GmMYB1 was considered as a direct target of GmSTF1/2. Expressing GmMYB1 in soybean hair roots and tobacco significantly promoted anthocyanin content. GmMYB1 could directly bind to the promoters of GmDFR, GmANS, and GmUFGT, thereby promoting their transcriptions. In addition, GmMYB1 interacted with GmbHLHA, and their interaction could enhance the functions of GmMYB1 in positively regulating anthocyanin accumulation. R3-MYB GmCPC-like was activated by GmMYB1 when anthocyanin was abundant. Expressing GmCPC-like significantly inhibited anthocyanin contents in soybean hair roots and tobacco. GmCPC-like inhibited anthocyanin accumulation mainly through interacting with GmMYB1 and GmbHLHA, and then decreased their positive roles in anthocyanin production. Taken together, the GmMYB1-GmbHLHA-GmCPC-like module finely regulates anthocyanin production in soybean sprouts.