Studies on the development of non-dairy probiotic foods and beverages are emerging. The optimal Lactobacillus and carbon resources were screened to improve the viability of probiotics in blueberry pomace. During fermentation, the total titratable acid and the viable counts were measured and peaked at 24 h, 15.75 mM and 11.59 Log CFU mL-1 respectively. Lactic acid content increased from 2.361 mg mL-1 to 6.334 mg mL-1, while citric acid content was decreased significantly. Additionally, the antioxidant activity was improved, which may be attributed to the increase of total phenols and flavonoids up to 4629.21 μg GAE mL-1 and 404.99 μg RE mL-1. Simulated gastrointestinal digestion in vitro showed that the total polyphenols were decreased slightly, while anthocyanins were increased. We also studied the cholesterol-lowing capability of fermented BPL and found that the cholesterol-clearance rate could reach 67.17%. Moreover, through mice weight-loaded swimming experiments, we observed that the physical strength of mice fed a fermented juice for one month was significantly better than that of the control group (p < 0.05). Therefore, this study provides a high value application of blueberry pomace and the fermented blueberry pomace with probiotics as a new type of probiotic food can furnish potentially value to human health.