Compound light is required for plant growth and development, but the response mechanisms of plants are undercharacterized and not fully understood. The present study was undertaken to evaluate the effect of supplemental light (green light, G; white light, W; yellow light, Y) added to red-blue light (RB) and sole W on the growth and photosynthesis of rapeseed seedlings. The results revealed that supplemental G/W improved the growth and photosynthesis of seedlings, but supplemental Y significantly reduced the photosynthetic rate and palisade tissue layer. Sole W caused similar responses in terms of growth, leaf development, oxidative damage, and antioxidant capability as supplemental Y. In total, 449, 367, 813, and 751 differentially expressed genes (DEGs) were identified under supplemental G, Y, and W and sole W, respectively, compared to RB. The DEGs under different lights were closely associated with pathways such as light stimulus and high-light response, root growth, leaf development, photosynthesis, photosynthesis-antenna proteins, carbohydrate synthesis and degradation, secondary metabolism, plant hormones, and antioxidant capacity, which contributed to the distinct growth and photosynthesis under different treatments. Our results suggest that Y is more likely substituted by other wavelengths to achieve certain effects similar to those of supplemental Y, while G has a more distinctive effect on rapeseed. Taken together, supplementation RB with G/W promotes the growth of rapeseed seedlings in a controlled environment.