Rudimental stubble height of rationing rice is one of important factors on high-yielding cultivation. Effects of rudimental stubble heights on the yield and source-sink characteristics of ratooning rice were studied in two-line hybrid rice Peiliangyou 210. Three rudimental stubble heights were arranged in the study, which were 40 cm, 20 cm, and 10 cm respectively. The results indicated that rudimental stubble heights affected source-flow-sink characteristics of ratooning rice significantly. With the decreasing of rudimental stubble heights, (1) the growing stage of ratooning rice was postponed, but stubble height, spike length and leaf area index (LAI) were increased, (2) the activities of leaf sucrose-phosphate synthetase (SPS) decreased, while the crop growth rate and the number and area of big vascular bundle of different internodes and the activity of catalase were increased during the grain filling stage. (3) the accumulation and output rates of non-structure carbohydrate content in stem and sheath, the ratio of grain number to leaf area and specific leaf weight, the spikelets per panicle and the yield were increased. In Changsha region, the suitable rudimental stubble height of two-line hybrid rice Peiliangyou 210 is 10 cm.