A pot experiment in phytotron with controlled temperature was conducted to examine the effects of low temperature (LT) on differentiation and retrogression of branches and spikelets and grain filling of rice during panicle initiation (PI). In this study, indica inbred rice called Zhongjiazao17 was planted and treated at 17 and 20 ℃ of LT during primary branches anlage differentiation (Ⅱ) and pollen mother cell meiosis stage (Ⅵ) of PI. The results showed that the numbers of differentiated and survived branches per panicle were significantly reduced under LT treatment compared with control, and the number of survived spikelets was significantly decreased by 7.2%-12.4%, but the numbers of retrograded branches and spikelets were increased. Moreover, LT affected significantly the development of floral organ such as pollen activity and anther dehiscence, and caused harmful grain filling, particularly at 17 ℃. The numbers of total differentiated and survived branches and spikelets were lower during Ⅵ (PI) than during Ⅱ (PI) under LT stress, but more retrograded secondary branches and spikelets (increased by 11.6%) were found during Ⅵ (PI) compared with Ⅱ (PI). Meanwhile, in contrast to Ⅱ (PI), the seed setting rate was significantly lowered by 3.7% during Ⅵ (PI), which was attributed to reductions in pollen activity, pollen grains on stigma, anther dehiscence coefficient and grain filling rate. LT stress impact on rice panicles was higher at 17 ℃ than at 20 ℃ during Ⅱ and Ⅵ (PI). The cultivation measure could be correspondingly strengthened and improved in practice.