The invention provides a culture method of selenium-enriched chlorella. Chlorella is taken as a fermentation algae to be subjected to seed activation, and activation culture conditions are that shaking culture is carried out, the rotational speed is 80 to 200r/min, the inoculation amount is 5 to 10%, the pH is 6.5 to 7.5, the temperature is 27 to 35 DEG C, and the time is 48 to 72h; the seed activation is divided into three levels, and amplification culture is carried out from low to high according to the amount needed for fermentation; the activated algae algae is inoculated to a fermentation culture medium to be cultured, light and air are introduced, the pH is 6.5 to 7.5, the inoculation amount is 5 to 10%, the culture temperature is 27 to 35 DEG C, the stirring rotational speed is 50 to 200r/min, and the culture time is 90 to 120h. 2mg/L of sodium selenite is added in the fermentation culture medium, so that the selenium enrichment concentration in the chlorella is about 66ug/g, and the dry weight reaches more than 4.59g/L, and is improved by 9.7 times, and necessary conditions are provided for the development of industrial fermentation and the like for the selenium-enriched chlorella.