Soil salinization is one of the major abiotic stresses threatening global agricultural development. To systematically evaluate the salt tolerance of rice germplasm across the whole growth period and screen elite salt-tolerant accessions, this study used 4,015 rice germplasm accessions. The experiments were conducted in the coastal saline-alkali area of Qinzhou, Guangxi. A natural salt-tolerance identification approach was adopted, combining multi-stage directional elimination, precise quantitative identification, and multi-index comprehensive evaluation. Salt tolerance was assessed at the germination, seedling and reproductive stages, and whole-growth-period salt tolerance was evaluated using principal component analysis (PCA)-based comprehensive scoring. The results showed that after three seasons of multi-stage directional selection at the reproductive stage, 544 accessions with relatively stable salt tolerance were obtained. Precise quantitative identification revealed that at the reproductive stage, the mean yield salt tolerance coefficient of Japonica rice (0.2085) was significantly higher than that of Indica rice (0.1187). At the germination stage, the mean relative germination rate under salt stress of Indica rice (0.4514) was significantly higher than that of Japonica rice (0.1040). At the seedling stage, the mean salt tolerance score of Indica rice (3.52) was lower (i.e., more tolerant) than that of Japonica rice (4.76), Indicating stronger seedling-stage salt tolerance in Indica rice. Significant but weak correlations were observed among the salt tolerance of the three growth stages (|r| = 0.12–0.24), confirming the developmental stage-specificity of salt tolerance. Based on PCA comprehensive scores, the tested germplasm was classified into five salt tolerance grades. Among them, 29 accessions were identified as grade 1 (extremely strong salt tolerance), all of which were Japonica rice, mainly originating from the northern Japonica-producing regions of China, including Jilin, Shandong, Anhui, Heilongjiang, Jiangsu, and Liaoning. Accessions such as ‘Tongnian No. 1’, ‘Longjing 1656’, and ‘Huijing 801’ exhibited excellent salt tolerance throughout the whole growth period and can serve as core parents for salt-tolerant rice breeding. The multi-stage precise identification system established in this study can effectively evaluate whole-growth-period salt tolerance in rice, and the strong salt-tolerant germplasm identified provides an important material foundation for breeding salt-alkali tolerant rice varieties.