Chongqing, the only non-endemic area of Huanglong disease, has been established firstly virus-free three-stage breeding system for quality Citrus variety in China. However, that the annual sunshine hours in Chongqing are few and unevenly distributed during the year prolongs the growth period in Citrus seedlings compared to other’s Citrus plantation areas. Therefore, this seriously restricts the developing speed of citrus nursery industry in Chongqing. Recently, the light emitting diode (LED) has been used as supplementary lighting to cultivate Citrus during the autumn and winter that can shorten the growth period of citrus seedling and accelerate the virus-free breeding of new variety. In order to investigate the effects of different LED light qualities on their seedlings growth, trifoliate orange (Poncirus trifoliata L. Raf) in sand culture were selected as materials. 2-month-old seedlings were exposed to 150 μmol·m-2·s-1 irradiance for a 16 h·d-1 photoperiod under white fluorescent lamp (FL) and the following six LED light, respectively: red light (R), blue light(B), 1∶1 ratio of red/blue (RB 1∶1), 4∶1 ratio of red/blue (RB 4∶1), 4∶1∶1 ratio of red/yellow/blue (RYB 4∶1∶1), white light (W). Their phenotypic and biomass indices were measured. Results showed that roots of seedlings were significantly longer, stem diameters (excluding RB 1∶1) were wider and leaves were narrower under composite LED light treatments than those under fluorescent lamp treatement. Compared with fluorescent lamp treatment, stem elongation were inhibited, along with decrease in leaf numbers and increase leaf thickness under RB 1∶1 and RB 4∶1 treatments, under which leaf length and area were increased. Furthermore, stem elongation, leaf number and leaf length increased, while leaf area enlarged, and leaf thickness decreased under RYB 4∶1∶1 treatment in comparison with fluorescent lamp treatment. Dry matter accumulation and biomass distribution of shoot and root were better under white LED light and high ratio red LED light treatments than those under monochromatic light treatments, particularly with the greatest shoot biomass and the minimum root/shoot ratio under RYB 4∶1∶1 treatment. So, it is concluded that RYB 4∶1∶1 treatment is the best choice for the matter accumulation and shoot growth of trifoliate orange seedlings. This can offer the theoretical evidence for the accurate supplemental lighting system on the season or area of lack light, especially in Chongqing.