The illumination system evaluation method with light quantum theory based on spectra makes light emitting diode(LED) plant lighting system repeatable in modern agriculture, which has practical significance. Based on the light quantum theory, a red/blue LED plant lighting lamp with freeform surface substrate is designed and its parameters are measured with a freeform surface substrate design method, which has high light efficiency and high uniformity, and the pulse width modulation drive method is used. Moreover, the significance of the traditional illumination design method in LED plant lighting is analyzed in detail by comparing the experimental results with the simulation results. The experimental result shows that the photosynthetic photon flux density uniformity of the designed lamp is approximately 80%, and the highest temperature is about 50 ℃. The light efficiency of the lamp can be regarded as 100%, when light diffusion plates and other secondary light distribution methods are not used, and it is 34.5% higher than that of the case when a diffusion plate is used. Energy consumption for plant illumination is reduced greatly. In addition, the use of the diffusion plate will reduce the photosynthetic photon flux density uniformity of designed lamp, but have little influence on light mixing uniformity. Consequently, the primary light distribution method with the freeform surface substrate is more suitable and practical than the secondary light distribution methods with the diffusion plates for the red/blue LED combination in plant lighting.