•The hydrophobic polyester shellac and WPI were used to encapsulate LGG.•The two-side effect of shellac on the probiotic microcapsules was revealed.•The lower drying rate and Tg of shellac were detrimental to viability during drying.•The addition of shellac improved storage stability by reducing hygroscopicity.•It's positive effect was more conducive to the long-term storage of probiotics. Heat shock and hygroscopicity are two main factors that resulted in low viability of probiotics in spray-dried microcapsules during storage. Hydrophobic polyester shellac was combined with whey protein isolate (WPI) to solve this problem. The results suggested that although the survival rate after drying decreased from 20.63% to 0.01% with increased shellac to WPI ratio, the 1:1 shellac-WPI provided the best protection among all samples during storage. The consistence between moisture-adsorption-isotherm and bacterial inactivation constants confirmed the moisture barrier effect of shellac under moderate humidity. Single-droplet drying and differential scanning calorimeter revealed that shellac addition reduced the drying rate and glass transition temperature of microcapsules, which in turn decreased the membrane integrity and growth capability of the probiotics after drying. This study revealed the dual effect of hydrophobic material on instant and long-term survival of spray-dried probiotic microcapsules, which provided new sight to the design of composite wall materials.