To investigate the effects of alkaline stress on leaf injury and seedling survival of japonica rice, and to clarify differences in alkaline tolerance among varieties from different geographic origins, a total of 437 japonica rice germplasm resources were evaluated for alkaline tolerance in an alkaline screening pool with a pH value of approximately 8.9 during 2016～2017, with repeated assessments conducted over two consecutive years. The dead leaf rate and dead seedling rate at the seedling stage were used as the primary indicators of alkaline tolerance. The results showed that both the dead leaf rate and dead seedling rate gradually increased with prolonged alkaline stress, and significant differences in alkaline tolerance were observed among different japonica varieties. The period of 15～25 days after alkaline stress treatment was identified as the critical stage for evaluating alkaline tolerance at the seedling stage, with higher phenotypic values, standard deviation, and coefficient of variation for dead leaf rate observed at 15 days, while those of dead seedling rate were higher at 25 days. Population-level analysis revealed a regional clustering pattern of alkaline tolerance, with japonica rice varieties from the northeastern rice-growing regions of China, particularly Heilongjiang and Jilin Provinces, showing lower dead leaf rate and dead seedling rates and thus stronger alkaline tolerance at the seedling stage. Cluster analysis based on dead leaf rate and dead seedling rate further indicated that the genetic relationships among japonica rice varieties were related to geographical distance and latitude distribution of their origins. Additionally, 20 alkaline-tolerant japonica rice germplasm accessions, including Kongyu 131 and Jijing 105, were identified, providing valuable genetic resources for the improvement of japonica rice varieties adapted to saline–alkaline soils.