Identification of new heat tolerant rice germplasm and breeding of new heat tolerant varieties are important for lessening the impacts of heat stress on rice production. Our previous study showed that rice 9311 was heat sensitive, while rice SDWG005 from Africa was heat tolerant. In this study, leaf morphology, microstructure and other physiological indexes of 9311 and SDWG005 were observed, tested and analyzed during or after 5 consecutive days treatment of high temperature stress (42℃/28℃, 12 h/12 h). The results showed that there were no significant changes in leaf morphology and microstructure, MDA content and superoxide dismutase content of SDWG005 at most time points of high temperature stress as compared with normal growth, and the content of soluble sugar and leaf proline increased significantly, whereas the leaves of 9311 were wilting after high temperature stress, the content of malondialdehyde and proline increased significantly or extremely significantly, the soluble sugar did not change significantly, and the activity of superoxide dismutase decreased significantly. The high temperature stress had no significant effect on photosynthesis of SDWG005 seedlings, but inhibited the photosynthesis of 9311 seedlings significantly. The chlorophyll content of SDWG005 and 9311 increased significantly or extremely significantly at some time points, and the biomass accumulation of SDWG005 increased under high temperature stress. The morphological and physiological basis of heat tolerance of SDWG005 is discussed in the present study, which will be helpful for breeding rice varieties with high heat tolerance using SDWG005 in future.