To elucidate the resistance of high-yield hybrid rice (Oryza sativa L.) at the seedling stage to low temperature, photosynthetic characteristics, such as membrane lipid peroxidation, fatty acid composition, and chloroplast ultrastructure, were investigated in a newly developed super-hybrid rice ('Liangyoupeijiu') and a traditional chill-sensitive hybrid rice ('Shanyou63'), with 20°C as the control condition and 10°C as the low temperature treatment. Chlorophyll content, oxygen consumption by photosystem I, and oxygen production by photosystem II in the thylakoid membrane mainly decreased under the low-temperature treatment. The malondialdehyde content of 'Liangyoupeijiu' decreased slightly, while increases in membrane lipid peroxidation were greater in 10°C-treated than in 25°C-treated 'Shanyou63' seedlings. The index of unsaturated fatty acids increased in the two cultivars, particularly in 'Liangyoupeijiu'. No severe chloroplast ultrastructure damage was observed under cold stress, but the number of osmiophilic granules in 'Shanyou63' increased rapidly. The results indicate that compared to 'Shanyou63', 'Liangyoupeijiu' is more chill-resistant at the seedling stage.