In order to clarify morphological and physiological mechanisms of cold tolerance at the booting stage for rice photo thermo sensitive genic male sterile (PTGMS) lines, by using the cold tolerant PTGMS line Y58S and four other key PTGMS lines widely used in the production, the effects of low temperature stress (17.5℃、10d) on seed setting rate, panicle traits, plant height, photosynthetic characteristics and antioxidant enzymes were studied in this experiment. The results showed that Y58S had the highest cold tolerance among the five PTGMS lines under the long-term cold stress. Comparing to the cold sensitive PTGMS lines C815S and Zhu1S, morphological and physiological mechanisms of cold tolerant line Y58S were as follows: higher seed setting rate and lower cold injury index; panicle length and plant height were reduced to a lesser extent; photosynthesis was effected not significantly by cold stress, the SPAD value and Pn value didn’t change significantly; SOD and POD activity were slighter decreased, MDA content and relative conductivity were less increased.