The effects of the core lipid, shell moisture, product processing, and storage conditions on the color and viable bacterial count of probiotic crystal ball products during storage were studied. The reasons for the browning and gradual decline in the viable bacterial count of the products during storage were analyzed, and the shell formulation of the probiotic crystal ball product was optimized. The results are as follows: at 37 ℃ and 65% RH, the lipid in the core does not change significantly during storage, but the probiotic powder crystals in the core noticeably brown. When the moisture content of the shell exceeds 14.10%, product browning is more obvious after two months of storage at 37 ℃ and 65% RH, and the viable bacterial count is lower than 106 CFU/g. When the moisture content of the shell is decreased to 10.30%, the probiotic crystal balls fracture. Exposing probiotics to high temperatures for two hours during product processing has no significant effects on the color of the probiotic powder in the core. Compared with 25 ℃ storage, 37 ℃ storage leads to more serious browning and more significant viable bacterial count reduction in the probiotic powder. The elongation at break of the outer shell is increased by optimizing the shell formulation, and rupturing of the product at low shell moisture content (3.45%) is avoided. After shell optimization, the viable bacterial count of the probiotic crystal balls is increased by 1.85-fold. The problems of browning and low viability of the probiotic crystal ball products during storage were effectively solved in this research. The results provide theoretical guidance for the industrial production of probiotic crystal balls.