Eleven anthocyanins in the blueberry anthocyanins powders (BAP) were identified and quantified by HPLC-DAD-ESI-MS. BAP microcapsules (MBAP) were produced by spray drying using high methyl pectin (HMP) combined with whey protein isolates (WPI) or soy protein isolates (SPI) in different proportions as wall materials. Generally, SPI/HMP combination was more efficient in increasing the encapsulation efficiency and Tg, and in decreasing the particle size and hygroscopicity of the microcapsules than WPI or HMP or WPI/HMP combination. Microcapsules created with 4% SPI + 2% HMP combination (MBAPc), possessed superior anthocyanin release behavior and antioxidant stability to those produced with 4% SPI alone (MBAPs). Both MBAPc and MBAPs had continuous release of anthocyanins throughout the simulated gastrointestinal digestion, and exhibited two first-order kinetics, but MBAPc exhibited higher stability than MBAPs and BAP, because it showed the longest half-life and the lowest anthocyanin degradation rate at 25 °C and 35 °C during 6-months’ storage.