In order to study the effects of root zone temperature on the main metabolites and chlorophyll content of maize seedlings, the spectral characteristics and chlorophyll content of two maize cultivars under three root zone temperature levels were determined by Fourier transform infrared spectroscopy and SPAD-502 chlorophyll meter. The results showed that different root zone temperature treatment had significant effects on the organic matter content of various organs of maize seedlings, but the degree of influence was different, and the general realization was root>stem>leaf. The transmission of wave number of maize seedlings in 3 330, 2 927, 1 639, 1 515, 1 350, 1 250 and 1 055 cm-1 was affected by the temperature of the root zone. The peak value was lower under medium temperature conditions and higher under the high temperature condition of the root zone, and the difference was most obvious at 1 055 cm-1. The FTIR infrared spectral characteristics of different varieties in the root zone temperature range are quite different, and SD902 has a large difference, while SD609 has a small difference. The temperature of root zone had significant effects on the root activity and chlorophyll content of different maize varieties, and both showed medium temperature (30 ℃)>control (24 ℃)>high temperature (36 ℃). In summary, appropriate increase of root zone temperature can significantly increase the content of chlorophyll, root activity, carbohydrates, especially polysaccharides in corn seedlings, as well as protein and nucleic acid content in stems and leaves, but excessive temperature will rapidly decrease the content of polysaccharides, root activity, lipids and chlorophyll. The increase in root zone temperature has a significant effect on the seedling metabolites of SD902 and SD609 corn varieties, and the SD902 is more sensitive to the temperature response in the root zone, and the SD609 has better heat resistance. The root zone temperature had the greatest effect on the roots of maize seedlings, and by effecting the roots absorption, material synthesis and material transport functions, and then affect the stalk, leaf organic matter and chlorophyll content.