To address the issues of probiotic activity loss during storage and feeding, as well as the limited efficacy of single probiotics, a solution was devised by embedding a mixture of Bacillus coagulans SN‐8 (SN‐8) and Saccharomyces boulardii SN‐6 (SN‐6) in a gel. The initial step involved screening the probiotic microcapsules' preparation method and wall material. Using sodium alginate and β‐cyclodextrin as composite wall material and chitosan as the outer coating material allowed for an embedding rate of 82.11% in composite probiotic microcapsules prepared by the air atomization method. Next, in vitro, simulated digestion experiments were conducted to determine the number of viable bacteria and the release rate of the microcapsules. The results showed that compared to the free strain, the mixed probiotic microcapsules retained a survival rate of 67.5% after 3 h of simulated gastric juice exposure and 70.56% after 42 days of storage at 4°C. This demonstrated higher survival rates and storage stability. The prepared probiotic microcapsules were then administered to dairy cows. 16S rDNA gene sequencing showed that consumption of the microcapsules reduced the number of harmful bacteria, such as Paeniclostridium, in the intestinal tract of dairy cows while accelerating the growth of beneficial bacteria, such as Bifidobacterium. In particular, this resulted in a significant improvement in the lactation performance of the cows, with a 4.5% increase in milk fat content, a 92.5% increase in milk protein content, and a 3.5% increase in milk urea nitrogen content (6.75 mL/dL). In conclusion, probiotic microcapsules can effectively regulate intestinal flora, improving milk production, and quality in dairy cows.