Early and late crops of South-China Indica rice cultivars, Hemeizhan, Huangsizhan and Yueguangsimiao, and three-line hybrid rice combiniations Tianyou312 and Tianyou390 were chosen in Guangzhou in 2009 to study the cold tolerance at the 5–6 phases of panicle differentiation, at initial heading stage, at flowering stage and at initial milking stage in the batanatrons (PGV–36). The results showed that chilling stress conducted at 5–6 phases of panicle differentiation, at initial heading stage and flowering stage decreased the plant height, the stem internodes length, the grain yield per panicle and the seed setting rate of South-China Indica rice cultivars and combinations. The rice cultivars and combinations responded differently to the chilling stress at different stages of growth and development. At the 5–6 phases of panicle differentiation but not other stages, the panicle length became shorter, and the total spikelets per panicle became fewer under chilling stress. The third internode under the panicle was shortened very significantly under chilling stress at the 5–6 phases of panicle differentiation and the first and second internodes became shorter at the initial heading and flowering stage. Incomplete panicle exertion was aggravated at the initial heading and flowering stage but not at the 5–6 phases of panicle differentiation. The cold tolerance of the tested materials was distinctive significantly different at different stages of growth and development, rice cultivars and combinations at initial milking stage showed the highest cold tolerance followed by flowering stage, initial heading stage and 5–6 phases of panicle differentiation. And for the same cultivar or combination, the cold tolerance was different at different stages, Tianyou390 showed high level of cold tolerance at the 5–6 phases of panicle differentiation stage and initial milking stage, and weak tolerance at the heading and flowering stage; Yueguangsimiao showed low level of cold tolerance at the 5–6 phases of panicle differentiation, and high tolerance at the heading and flowering stage.