Abstract: Low temperatures are one of the main limiting factors in the development of agricultural facilities in North China. Farmers need cheap and convenient agronomic measures to improve tomato resistance to low temperatures. The aim of this study was to investigate the effects of nano-Si on root system architecture and the accumulation mechanism of non-structural carbohydrates of tomato seedlings at low temperatures. In this study, the tomato cultivar ‘Zhongza 9’ was cultivated by substrate cultivation and was used as the test material, and the effects of leaf spraying nano-Si (0 mg∙L⁻¹ and 100 mg∙L⁻¹) at room temperature (25 ℃/16 ℃, day/night) and low temperature (15 ℃/6 ℃, day/night) on tomato biomass, root system architecture, photosynthetic capacity, and non-structural carbohydrates contents were studied. The results showed that: 1) At low temperatures, the biomass, total root length, root tips number, photosynthetic pigment content, and net photosynthetic rate of tomatoes were significantly decreased (P<0.05), while the contents of soluble sugar, sucrose, and starch were significantly increased (P<0.05), and shoot fresh weight, net photosynthetic rate, and total root length were decreased by 48.60%, 66.88%, and 65.49%, respectively (P<0.05). 2) Application of nano-Si significantly increased tomato biomass, root activity, root tips number, fractal dimension, net photosynthetic rate, and non-structural carbohydrates contents at room temperature and low temperature (P<0.05), whereas application of nano-Si at low temperatures increased the root tips number, net photosynthetic rate, and leaf soluble sugar content by 35.25%, 48.24%, and 75.69%, respectively (P<0.05). In conclusion, low temperatures severely restrict photosynthesis, root growth, and transport of non-structural carbohydrates in tomato leaves, and root system architecture parameters tend to change in directions that are not conducive to plant growth. The application of nano-Si could improve the cold resistance of tomatoes by promoting the synthesis of photosynthetic pigments, increasing the photosynthetic rate and root activity, improving root system architecture, and increasing the synthesis of non-structural carbohydrates.