This study aims to assess the salt tolerance of perennial rice varieties (lines) ‘PR23’, ‘PR24’, ‘PR25’, ‘PR26’, ‘PR101’, ‘PR107’, and ‘PR109’, and to screen out elite salt-tolerant germplasm. The experiment employed NaCl solutions at concentrations of 0, 50, 100, 150, and 200 mmol/L to conduct salinity stress treatments on perennial rice varieties (lines) and the parent ‘RD23’. The vitality parameters (seedling height, root length, fresh weight, dry weight, etc.) and salt tolerance coefficients of varieties were determined under different NaCl concentrations. Principal component analysis (PCA) and the membership function method were used to comprehensively evaluate the salt tolerance performance of the varieties (lines). The results showed that: (1) significant differences in salt damage levels among varieties (lines) were observed when NaCl concentration reached 150 mmol/L. Among all the phenotypic traits associated with salt stress, except for root length, all other traits under the 150 mmol/L NaCl treatment showed significant differences from the control group (P < 0.05), establishing this concentration as the optimal level for screening salt tolerance in perennial rice during the seedling stage. (2) PCA of the relative values of salt tolerance traits under the 150 mmol/L NaCl treatment generated membership function values. Combining with the principal component variance contribution rate weight, the comprehensive evaluation D value was obtained, showing that ‘Yun Da 107 (PR107) ’exhibited the strongest comprehensive salt tolerance ability at the seedling stage, while ‘PR101’ showed the weakest salt tolerance capacity. Other varieties (lines) had intermediate salt tolerance levels. This study provides high-quality germplasm resources for rice salt tolerance breeding and lays the foundation for future improvements in rice salt tolerance. This study not only identifies elite salt-tolerant rice germplasm resources through phenotypic and genotypic assessments, laying a foundation for genetic improvement of rice salt tolerance, but also provides critical data support for further research on salinity stress tolerance mechanisms.