Selenium was an essential micronutrient for human beings，and eating selenium-rich agricultural products had the effects of preventing diseases，enhancing immunity and anti-aging. Polygonatum had strong biological enrichment ability for selenium，and using selenium fertilizer to enhance Polygonatum was one of the safe and effective ways to obtain selenium rich agricultural products，so it had great significance to study the effects of selenium fertilizer on the growth of Polygonatum and its rhizosphere soil nutrients and enzyme activities. A pot experiment was conducted by Polygonatum to study the effects of three different types of fertilizers(ordinary earthworm fertilizer，earthworm with inorganic selenium fertilizer，earthworm with organic selenium fertilizer) on the biomass，leaf growth，stem diameter，plant height，root number，polysaccharides，selenium content，selenium form，rhizosphere soil nutrients，and enzyme activity of Polygonatum seedlings. The results showed that the application of ordinary earthworm fertilizer and earthworm with inorganic selenium fertilizer in the soil had no significant promoting effect on the growth of Polygonatum seedlings compared to no fertilization treatment. The application of earthworm organic selenium fertilizer significantly improved the growth indicators of Polygonatum，such as biomass，leaves，plant height，rooting number and polysaccharides. The application of exogenous selenium fertilizer significantly increased the selenium content of Polygonatum. The total selenium and organic selenium content in the organic selenium fertilizer treatment of earthworms were 1.38 and 1.56 times higher than those in the inorganic selenium fertilizer treatment，respectively. The application of earthworm with organic selenium fertilizer was more conducive to the accumulation of total selenium and organic selenium in Polygonatum. Earthworm with organic selenium fertilizer promoted the release of alkali-hydrolyzed nitrogen and available potassium in the rhizosphere soil of Polygonatum. Correlation analysis showed that the increase in soil alkali-hydrolyzed nitrogen and available potassium may be one of the reasons why earthworm organic selenium fertilizer promoted the growth and quality improvement of Polygonatum. The enzyme activity of Polygonatum rhizosphere soil exhibited different dynamic responses to different selenium fertilizers. Exogenous selenium fertilizers significantly enhanced the activity of soil urease and sucrase. Organic selenium fertilizers were more conducive to promoting the growth and reproduction of soil microorganisms and improving soil enzyme activity compared to inorganic selenium fertilizers. In summary，earthworm organic selenium fertilizer was an ideal growth-promoting fertilizer and selenium strong fertilizer for the seedling stage of Polygonatum. Replacing the ordinary earthworm fertilizer or the earthworm with inorganic selenium fertilizer by the earthworm with organic selenium fertilizer is expected to become a main way to cultivate selenium rich agricultural products in the future.