The objective of this study was to reveal the difference of dry matter accumulation and its distribution, and the main morphological and physiological characteristics in roots between indica and japonica super rice, and their relationship with yield formation. A field experiment was conducted using two main representative super hybrid indica combinations and two conventional japonica super rice varieties in wheat-rice double cropping regions. Dry weight of root, total root length, root number, root volume, root absorbing area, root germination ability and root bleeding intensity after heading for both single stem and population, root-shoot ratio, single root length, root diameter, root density, root bleeding per spikelet, root distribution in the soil at heading and yield components were analyzed systematically. Results showed as follows: (1) For the whole growth duration, root-shoot ratio, single root length, root germinating number, root germinating volume, root germinating dry weight, root bleeding per spikelet, number of panicles, total spikelets, seed-setting rate and grain yield of japonica rice were higher thanthose of indica rice, while root diameter, spikelets per panicle and 1000-grain weight followed an opposite tendency, with root-shoot ratio, single root length, root bleeding per spikelet, number of panicles, spikelets per panicle, seed-setting rate and grain yield being a significantly different. (2) Before heading, dry weight of root, total root length, root number, root volume and total absorbing surface area of root per stem and root density of japonica rice were lower than those of indica rice, though not significantly, and higher than those of indica rice significantly at maturity. (3) Before jointing, active absorbing surface area per stem and ratio of active absorbing surface area to total absorbing surface area in japonica rice were less than those in indica rice significantly, which showed an opposite trend after jointing. (4) Population indicators of morphological and physiological characteristics of japonica rice except for population root dry weight at jointing and root number of population at jointing and heading were higher than those of indica rice significantly. (5) Root bleeding intensity during 0–35 d after heading was higher in japonica rice than in indica rice significantly whether it was based on a single stem or population. (6) Ratio of root dry weight in the 0–10 cm layer to total root dry weight was lower in japonica rice than in indica rice significantly, with an opposite trend for the >10 cm layer, which indicated the deep-rooted characteristic of japonica rice can strengthen its resistance to lodging and premature senescence. Compared with super hybrid indica rice, root growth advantages of conventional japonica super rice after heading were increased, especially for population growth advantages, and all the root morphological and physiological characteristics indicators of japonica rice at maturity were better than those of indica rice, which is the important cause and assurance for high-yielding formation of japonica rice.