The reduction of emergence rate under hypoxia stress is a major constraint to safe production of direct-seeded rice. It is of great significance to establish an accurate and efficient identification method for anaerobic germination tolerance and to screen rice germplasm resources with strong germinability under submerged condition for breeding new cultivars adapted to direct seeding. In this study, 20 rice varieties were used as the test materials, and the germinability under submerged condition was evaluated under different depths of waterlogging (3 cm, 6 cm, 9 cm, 12 cm, 15 cm and 18 cm), different temperature conditions (20 ℃, 25 ℃ and 30 ℃) and different days of waterlogging (3 d, 5 d, 7 d, 9 d, 11 d, 13 d and 15 d), and corresponding coleoptile length was deployed as an index for evaluating anaerobic tolerance at the germination stage. The results showed that the critical depth of flooding was 6 cm for japonica rice and 9 cm for indica rice, with a significant difference between the two subspecies. Under the condition of 30℃, the coleoptile length showed the highest interquartile range among varieties in the gradient temperature treatment. Therefore, it is considered that 30 ℃ is the optimum temperature for identification anaerobic tolerance at the germination stage. The gradient days of waterlogging treatment showed that coleoptile length shown the highest interquartile range after 11 days of waterlogging stress. Therefore, it is considered that 11 day after waterlogging treatment was the best time point to investigate germinability under submerged condition in rice. In summary, a simple and effective method for screening anaerobic germination tolerance was established, with pure water isolated from air at 30 ℃, more than 9 cm depth of waterlogging, and coleoptile length was measured at the 11th day of waterlogging, which provided a method basis for large-scale identification of rice germplasm resources with strong germinability under submerged condition. By taking use of the aforementioned pipeline, 140 germplasm resources released from different regions were screened, and 6 varieties with high anaerobic germination tolerance (coleoptile length≥55 mm) were found, which might provide a material basis for underlying the genetic mechanism and utilization in breeding program adapted to direct seeding.