After anthocyanins were extracted from plant cells, deep eutectic solvent (DES) spontaneously promoted the stability of anthocyanins. To better understand the stability of anthocyanins in DES, and in particular the role of co-extracted cell wall polysaccharides, blueberry anthocyanins were initially recovered with four different DESs (choline chloride (CC):citric acid (CA), CC:lactic acid (LA), CC:glycerol (G) and CC:ethylene glycol (EG)). Then, the impacts of DES formulation and co-extracted polysaccharides on the stability of blueberry anthocyanins were systematically evaluated. Results showed that the extraction efficiency for anthocyanins was closely related to the polarity of DES, with CC:CA exhibiting the highest total anthocyanins content. Twelve anthocyanins were identified, and DESs showed selectivity for different anthocyanins. DESs co-extracted different proportions of low-methoxyl pectin rich in homogalacturonan (HG) or rhamnogalacturonan I (RG I) backbone structure together with hemicellulose. The stability of anthocyanins in DESs was discriminated by the degradation kinetic parameter (half-life of degradation-t1/2). The DES formulation did not fully explain the variation in t1/2 values. Instead, the t1/2 values were found to correlate positively with HG and hemicellulose contents, resulting from the interactions between anthocyanins and polysaccharides. Except for CC:G that showed the highest t1/2 at temperatures ≥ 80 °C, CC:CA afforded higher t1/2 under varied temperatures (≤60 °C), pH and light exposure. Finally, the anthocyanin-containing DESs exhibited biocompatibility and antioxidant capacities. These results offer new insights for the understanding of the enhanced stability of anthocyanins in DES, and promote the direct application of anthocyanin-containing DESs in food-related fields.