To investigate the effects of Na⁺ and K⁺ content and distribution of the seedling shoot and root on the biomass accumulation and salt tolerance in rice， 51 rice germplasm accessions were analyzed under salt stress treatment by using Yoshida culture solution containing 125 mmol/L NaCl. Five morphological parameters including salt tolerance score （STS）， relative root length （RRL）， relative shoot dry weight （RSDW）， relative root dry weight （RRDW）， shoot water content （SWC）， and six ion indexes， namely shoot Na⁺ content （SNC）， root Na⁺ content （RNC）， shoot K⁺ content （SKC）， root K⁺ content （RKC）， shoot Na⁺/K⁺ ratio （SNa⁺/K⁺） and root Na⁺/K⁺ ratio （RNa⁺/K⁺） were measured. On the basis of principal component analysis （PCA）， with membership functions and weighted standard deviation coefficient method， a comprehensive evaluation D value for each rice germplasm accession was obtained. Specific primers for amplifying the coding region of SKC1 were applied for sequencing， alignment and haplotype analysis. SNC was significantly negatively correlated with other morphologic indexes except RRL， and STS was found to be significantly negatively correlated with SNC， RNC and SNa⁺/K⁺. Meanwhile， significant positive correlations among STS， RSDW， RRDW and SWC were revealed by correlation analysis. PCA with 11 indexes suggested four major components， with a cumulative contribution rate of 82.093%. Six key indexes， including RSDW， STS， RRDW， SNC， SNa⁺/K⁺ and RNC， were selected based on the loadings of 11 indexes in PC1. Combined with the linear regression analysis between the D value and these six indexes， it was found that STS and SNa⁺/K⁺ may be the key factors affecting salt tolerance by maintaining growth and ion balance in rice seedlings respectively， with a great regression coefficient. The diversity analysis of SKC1 coding sequence suggested nine different haplotypes of 51 rice germplasm accessions. The Hap1 detected in Koshihikari was dominant in japonica rice accessions， and the Hap7 detected in Nona Bokra was dominant in indica and Aus rice accessions. Collectively， the results gained from this study provided a theoretical foundation for identifying the salt-tolerant rice germplasm accessions in ion homeostasis.