Submergence stress is a major factor limiting the seedling establishment rate of direct-seeded rice, and elite germplasms with rapid coleoptile elongation under submerged conditions exhibits greater adaptability to direct-seeding systems. Autotetraploid rice possesses polyploidization advantages such as enlarged grains, strong heterosis, and enhanced stress tolerance; however, its low fertility has constrained its research and application. The emergence of fertile neo-tetraploid rice, which overcomes the sterility bottleneck and retains the above-mentioned polyploidization advantages, holds promise as a source for elite submergence-tolerant germplasm. In this study, 380 neo-tetraploid-derived lines were evaluated for submerged tolerance during germination, and 11 tolerant accessions were identified. Under submergence stress (8 cm depth of water), the coleoptiles of these accessions elongated rapidly, reaching lengths 1.94‒2.90 times that of the control variety H441. In subsequent pot soil submerged assays, deep submergence significantly reduced the seedling establishment rate of the control H441 to 30.34%, whereas the tolerant lines maintained seedling establishment rate of 45.34%‒65.34%, comparable to shallow-water conditions. Cytological observations revealed that cell lengths in both the middle and tip regions of the coleoptiles were significantly greater in the tolerant accessions than in the control. Physiological measurements indicated that the coleoptiles of tolerant accessions exhibited higher superoxide dismutase activity under submergence stress. In addition, the tolerant lines retained desirable agronomic traits of neo-tetraploid rice, including normal seed setting and relatively large grain size. This study establishes a screening system for submergence-tolerant germplasm in tetraploid rice, and the elite accessions obtained provide valuable materials for future investigations into genetic mechanisms underlying submergence tolerance and for breeding submergence tolerant polyploid rice varieties.