The effect of long-term dietary supplementation with rutin on the lactation performance, ruminal fermentation and metabolism of dairy cows were investigated in this study. Twenty multiparous Chinese Holstein cows were randomly divided into four groups, and each was offered a basal diet supplemented with 0, 1.5, 3.0 or 4.5 mg rutin/kg of diet. The milk yield of the cows receiving 3.0 and 4.5 mg rutin/kg was higher than that of the control group, and the milk yield was increased by 10.06% and 3.37% (p < 0.05). On the basis of that finding, the cows supplemented with 0 or 3.0 mg rutin/kg of diet were used to investigate the effect of rutin supplementation on blood metabolites and hormone levels. Compared with the control group, the serum blood urea nitrogen (BUN) concentration of the 3.0 mg rutin/kg group is significantly decreased (p < 0.05). In another trial, four adult cows with permanent rumen fistula and duodenal cannulae were attributed in a self-control design to investigate the peak occurrence of rutin and quercetin in different parts of the gastrointestinal tract, ruminal fermentation and microbial population in dairy cows. The cows supplemented with 3.0 mg rutin/kg in the diet differed from the control period. Samples of rumen fluid, duodenal fluid and blood were collected at 1, 2, 3, 4, 5, 6, 7 and 8 h after morning feeding. Compared to the control group, the pH, ammonia nitrogen concentration, number and protein content of rumen protozoa and blood urea nitrogen were lower, but the concentration of total volatile fatty acid (TVFA), microbial crude protein (MCP) and serum lysozyme content were higher for the cows fed the rutin diets. The addition of 3.0 mg rutin/kg to diets for a long term tended to increase the milk yield and improve the metabolism and digestibility of the dairy cows.