Abstract Currently, the information about different characteristics of high yield formation between inbred japonica super rice cultivars (IJSRC) and inter-sub-specific hybrid super rice cultivars (IHSRC) is quite limited. In this present study, the different characteristics of high yield formation between IJSRC (Nanjing 44 and Ningjing 3) and IHSRC (Yongyou 12 and Yongyou 15) were further investigated. Our results indicated that compared with IJSRC, IHSRC displayed a significant increase of the total spikelet numbers per square meter and had higher yields (exceeding 13.18%), which might be related to IHSRC’s more efficient use of temperature and light during the stage from elongating to heading. Moreover, with the strong ability to tiller, the leaf area indexes of IHSRC at elongating, heading and maturity stages were larger than those of IJSRC. Leaf area durations of IHSRC were also higher, in particular during the periods from elongating to heading and from heading to maturity. Although the percentages of above-ground biomass accumulation in IJSRC and IHSRC were similar, IHSRC accumulated more above-ground biomass during the periods from elongating to heading and from heading to maturity. At 30 days after heading, the photosynthetic rate, chlorophyll content and the root oxidation activity of IHSRC were significantly higher. In addition, the photosynthetic functions of IHSRC flag leaves were 6–8 days longer than those of IJSRC flag leaves. Although the yields of IHSRC were significantly higher than those of IJSRC, no differences in yield per day between two types of super rice were observed because of more days from sowing to maturity in IHSRC. Therefore, we concluded that both IJSRC and IHSRC had high yield per day, and the final yield depended on not only the characters of rice related to high yield formation but also the utilization of temperature and light resources in the ecological environment during their growth duration.