Probiotics such as Bifidobacterium spp. generally possess important physiological functions. However, maintaining probiotic viability is a challenge during processing, storage, and digestive transit period. Microencapsulation is widely considered to be an attractive approach. In this study, B. animalis F1–7 microcapsules and B. animalis F1–7-HMO microcapsules were successfully prepared by emulsification/internal gelation with high encapsulation efficiency (90.67 % and 92.16 %, respectively). The current study revealed that HMO-supplemented microcapsules exhibited more stable lyophilized forms and thermal stability. Additionally, a significant improvement in probiotic cell viability was observed in such microcapsules during simulated gastrointestinal (GI) fluids or storage. We also showed that the individual HMO mixtures 6′-SL remarkably promoted the growth and acetate yield of B. animalis F1–7 for 48 h (p < 0.05). The synbiotic combination of 6′-SL with B. animalis F1–7 enhanced SCFAs production in vitro fecal fermentation, decreasing several harmful intestinal bacteria such as Dorea, Escherichia-Shigella, and Streptococcus while enriching the probiotic A. muciniphila. This study provides strong support for HMO or 6′-SL combined with B. animalis F1–7 as an innovative dietary ingredient to bring health benefits. The potential of the synbiotic microcapsules with this combination merits further exploration for future use in the food industry.