This study evaluated the effects of dietary yeast culture (YC) supplementation on rumen microbiota and lactation performance in dairy goats. Twenty mid-lactation dairy goats were selected and divided into two groups: the control (CON) group was fed a basal diet; the YC group was supplemented with 10 g of YC in 1 kg of basal diet. The administration of YC was associated with a significant increase in dry matter intake, milk yield, milk protein yield, and milk lactose yield in dairy goats (P < 0.05). Additionally, serum total protein, albumin, creatinine, glucose, superoxide dismutase, and catalase levels were increased (P < 0.05). Furthermore, there was an increase in rumen pH and NH3-N levels (P < 0.05), while volatile fatty acid levels were observed to decrease (P < 0.05). The study found no significant difference in the α-diversity of bacteria and fungi between the YC and CON groups (P > 0.05). However, 15 bacterial genera and 13 fungal genera were upregulated (P < 0.05), while 4 bacterial genera and 11 fungal genera were downregulated (P < 0.05) in the YC group. The relative abundance of pathogenic fungi Dipodascus and Gibberella decreased (P < 0.05). Correlation analysis revealed that the bacterial genera were not significantly correlated with lactation performance (P > 0.05), whereas fungal genera Dipodascus and Gibberella were significantly (P < 0.05) correlated with lactation performance. In conclusion, the study demonstrated that YC can influence the rumen microbial composition, reduce the abundance of harmful fungi in the rumen, and improve lactation performance in dairy goats, suggesting that the addition of YC to dairy goat diets has good application prospects.