The invention relates to a method for preparing koumiss by employing sectioned inoculation fermentation of yeast and lactobacillus. The method comprises the following steps: 1) blending milk liquid from 6-20% of skimmed milk powder, 6-12% of white sugar and the balance of water; 2) carrying out a first disinfection; 3) cooling to 37-43 DEG C; 4) carrying out a first fermentation: inoculating 0.005-0.1 wt% of direct vat set lactobacillus starter in the cooled milk liquid and fermenting for 4-12 h under 37-43 DEG C, wherein the direct vat set lactobacillus starter is a mixture of Lactobacillus bulgaricus and Streptococcus thermophilus according to a live bacterium number ratio of 1:1; 5) carrying out a second fermentation: inoculating 0.005-0.1 wt% of Saccharomyces cerevisiae into the milk liquid treated with the first fermentation and fermenting for 48-72 h under 28-32 DEG C to form a broth; 6) blending 0.2-0.8% of stabilizing agent, 2-4% of white sugarm, 80-90% of broth and the balance of water to form a blending liquid; 7) homogenizing; and 8) carrying out a second disinfection. The method for preparing koumiss of the invention can substantially reduce vinasse flavour and bitter taste of the koumiss, and stable distribution of lactoprotein is relatively uniform in the fermentation process to increase alcohol content.