Temperature is one of the abiotic factors limiting growth and productivity of plants. In the present work, the effect of low non-freezing temperature, as an inducer of "chilling resistance", was studied in three cultivars of rice (Oryza sativa L.), japonica cv. 9516 (j-9516), the two parental lines of superhigh-yield hybrid rice between subspecies,Peiai/E32 (ji-PE), and the traditional indica hybrid rice Shanyou 63 (i-SY63). Leaves of chill-treated rice showed chilling-induced resistance, as an increase of their low-temperature tolerance was measured using chlorophyll fluorescence measurements, revealing a change in photosystem Ⅱ (PSⅡ) efficiency. After 5 d of exposure to 11℃ under low light (100 μ mol·m-2·s-1), levels of unsaturated fatty acids in PSⅡ thylakoid membrane lipids decreased during the initial 1-2 d, then increased slowly and reached 99.2％, 95.3％ and 90.1％ of the initial value (0 d) in j-9516,ji-PE and i-SY63, respectively, on the fifth day. However, under medium light (600 μmol·m-2·s-1), all cultivars experienced similar substantial photoinhibition, which approached steady state levels after a decline in levels of unsaturated fatty acids in PSII thylakoid membrane lipids to about 57.1％, 53.8％ and 44.5％ of the initial values (0 d) in j-9516,ji-PE and i-SY63 on the fifth day. Under either chilling-induced resistance (the former) or low temperature photoinhibition (the latter) conditions, the changes of other physiological parameters such as D1 protein contents,electron transport activities of PSII (ETA), Fv/Fm, xanthophyl cycle activities expressed by DES (deepoxide state)were consistent with that of levels of unsaturated fatty acids in PSⅡ thylakoid membrane lipids. So there were negative correlations between saturated levels of fatty acids (16:1(3t), 16:0, 18:0), especially the 16:1(3t) fatty acid on thylakoid membrane and other physiological parameters, such as D1 protein contents, ETA and (A+Z)/(A+V+Z). A specific role of desaturation of fatty acids and the photoprotective pigments of the xanthophyl cycle, leading to an acclimation response in thylakoid membrane lipids may be involved. We conclude that chilling-induced resistance is accelerated by the unsaturation of thylakoid membranes, and the ability of rice plants to cold-harden can be enhanced by genetic engineering.