To understand the response of leaf structure and photosynthetic characteristics of seedlings to different light, we apply four LED lights, red, blue, yellow, green as the light source to 30 d and 60 d Houttuynia cordata Thund. Seedlings. Compared with that treated by white light (CK), the leaf structure under yellow light, blue light and red light treatments showed advantages in leaf thickness, upper epidermis and lower epidermis thickness, palisade tissue and spongy tissue thickness, while that treated by green light displayed disadvantages. And compared with 30 d seedlings growth, the increment of leaf structure on 60 d seedlings by blue light was most among all the treatments. The increment of mount of chlorophyll a, chlorophyll b and total chlorophyll under the blue light treatment was the highest followed by the treatments of white, yellow, red, and green light. Seedling leaf photosynthetic rate showed significant differences under different lights, the photosynthetic fluorescence parameters (F0, Fm, qP and NPQ) of seedlings under blue light treatment were greater than those of white light treatment, which indicated blue light treatment was most suitable for enhancing leaf structure and photosynthetic fluorescence characteristics of Houttuynia cordata Thunb.