The production of Indica rice in China is facing severe challenges from biological and non-biological disasters such as pests, diseases, and heat stress. There is an urgent need to explore elite Indica rice germplasm resources that can adapt to climate change for current and future rice breeding. In this study, 654 indica rice varieties of different periods from various southern provinces of China were selected as experimental materials. The main agronomic traits were evaluated in four different environments, including Nanning in Guangxi, Guiyang in Guizhou, Jingzhou in Hubei, and Hangzhou in Zhejiang. Additionally, heat tolerance at the seedling stage was assessed in artificial climate incubator. The results showed that there were obvious phenotypic differences in these agronomic traits in the different environments. The rice yield per plant in Jingzhou and Hangzhou with higher latitude and lower altitude was higher than that in Guiyang and Nanning with lower latitude and higher altitude. The altitude of the Guiyang is significantly higher than that of the other sites, and the summer temperature is lower than that of the other sites, therefore, compared to the other sites, the seed setting rate, thousand grain weight, and grain width of rice have increased, while the plant height, panicle length, panicle number per plant, and yield per plant have decreased. Under multiple environmental conditions, the phenotypic values of panicle number per plant, panicle length, thousand grain weight, grain length, and grain width are relatively stable, followed by heading days, plant height, seed setting rate, and yield per plant, while the stability of grain number per panicle is poorer. The stability coefficients of heading days, plant height, seed setting rate, and yield per plant for Indica rice varieties in different periods decrease with the increase of breeding periods, indicating that with the progress of periods, the ecological adaptability of the varieties gradually tends to strengthen. The comparison of phenotypes of Indica rice varieties in different periods indicates that the phenotypic traits of Indica rice varieties have been genetically improved overall towards larger panicle, more grain, longer grain, higher yield, and stronger heat tolerance. The genetic relationship between the varieties in Periods II (varieties developed before 1980) and Periods III (varieties developed between 1980 and 1999) was relatively closer, followed by that between the varieties in Periods II, Periods III and Periods I (landraces), while that between the varieties in Periods IV (varieties developed after 2000) and other periods'' were relatively further. Thirty varieties such as Guihuazhan, Shangcun Zao, Huanan 15 and Ganzaoxian 45, were identified, which had better adaptability to the multiple environments and could be used as parent materials for future rice breeding.