Microbial administration has been used successfully to improve host health. However, the positive effects of endogenous microbials are still underexplored. This study investigated the effects of bovine Lactic acid bacteria and yeast on the milk production, quality and digestive tract microbiome of dairy cows. Lactobacillus plantarum Y9, Pichia kudriavzevii T7 and Candida glabrata B14 isolated from high-yielding dairy cows were selected to feed low-yielding Holstein cows. Pichia kudriavzevii T7 could significantly increase milk yield, meanwhile, Pichia kudriavzevii T7 and Candida glabrata B14 could obviously reduce the number of somatic cell counts (SCC). However, slight differences were found in milk fat, protein, lactose and SNF (solids not fat) percentage. High throughput sequencing showed that the dominant bacteria were Prevotella and Ruminococcaceae in rumen and feces, respectively, and the dominant fungi were Penicillium, Aspergillus and Trichoderma in both samples, before and after feeding the microbial addition. Nonetheless, microbial addition changed the abundance and structure of the microbiome in the digestive tract. Our data showed bovine yeast and LAB were beneficial for improving performance and regulating the microbial structure of dairy cows. This study was expected to enrich the knowledge of the digestive tract microbiome in dairy cows and provide a feasible strategy for the further utilization of bovine microorganisms.