Intercropping can increase the utilization rate of light and water and can also improve plant growth. The objective of this study was to investigate the growth and selenium (Se) content in seedlings of three genotypes of cherry tomato under intercropping while applying Se. The pot experiment was conducted in a greenhouse. The monoculture of red, yellow and purple cherry tomato; among the three genotypes of cherry tomatoes, intercropping of two genotypes with each other, at the same time intercropping of three genotypes. These results show that the biomass increased under intercropping compared with monoculture. The chlorophyll b content of purple cherry tomato increased in different intercropping combinations. Furthermore, the net photosynthetic rate, stomatal conductance, and transpiration rate of purple were increased by intercropping with red and purple cherry tomatoes. The soluble protein and soluble sugar contents in yellow and purple cherry tomato increased by 49.13% and 8.37%, respectively, under mutual intercropping. Similarly, soluble sugar increased in purple cherry tomato by intercropping with yellow and red. The activities of superoxide and peroxidase in red and yellow cherry tomato seedlings were higher in all intercropping combinations than in monoculture, whereas free proline content and relative conductivity in all cherry tomatoes decreased. The Se content of roots, stem, and leaves in seedlings increased with intercropping. Therefore, intercropping can improve the growth and Se content of cherry tomatoes, and the combination of red, yellow and purple is better, which can be used to cultivate strong seedlings.