Anthocyanins are vital secondary metabolites contributing to fruit pigmentation and antioxidative properties. While light is a well-known regulator of anthocyanin biosynthesis, the molecular basis of light-independent anthocyanin accumulation remains underexplored. In this study, integrated analysis of metabolome and transcriptome showed that the anthocyanin content in blueberry (Vaccinium corymbosum ‘Bluetta’) fruit was slightly decreased by light-impermeable bagging treatment, while anthocyanin biosynthetic genes were transcriptionally inhibited to different levels, suggesting a slight influence of the bagging treatment on anthocyanin accumulation. Further observation showed that fruit bagging did not alter ethylene production but decreased ABA content. Noticeably, two VcMYBA/MYB1s were not transcriptionally altered by the light-impermeable bagging treatment. Consistently, histochemical GUS analysis and pharmacological manipulation suggested light-independent and ethylene-inducible expression of VcMYBA/MYB1. Moreover, WGCNA analysis revealed 3759 genes positively associated with MYBA/MYB1 such as ethylene-associated genes, etc. Additionally, VcbZIP55s and VcCOP1s were activated and inactivated by the bagging treatment, respectively. These findings provided a framework of light-independent anthocyanin biosynthesis in blueberry fruit.