Rice is a salt sensitive plant, and soil salinization has a significant impact on rice yield. Therefore, exploring excellent haplotypes of salt tolerant genes and creating excellent salt tolerant germplasm are of great significance for rice breeding. This study firstly identified 236 core germplasm samples from the 3K rice database for salt tolerance investigation during seedling stage and whole growth period in the field. A strong salt tolerant germplasm ''71011'' from Australia was identified. This germplasm survived for 25.5 days and had a salt tolerance level of 5.2 under 150mM NaCl treatment conditions, 100% survival rate under 0.3-0.5% salt treatment in the paddy field. Using the 236 core germplasm population, haplotype analysis was conducted on 20 reported salt tolerance genes. A total of 8 genes, including AKT1, CPK12, MYB48, P5CS1, SIK1, SKC1, SNAC1, and HKT1, was identified that had haplotypes associated with salt tolerance. Then, one salt tolerant rice variety ‘Yanfeng 47’ and one normal variety ‘Nongken 57’ were selected as parents for recombinant inbred lines construction. Finally, three molecular markers were designed for elite haplotypes of three genes, AKT1, MYB48, and HKT1. These molecular markers were confirmed by PCR and qRT-PCR. We innovated three high salt tolerance lines by aggregating elite haplotypes of salt tolerant genes by molecular marker assistance breeding. Our results provided available germplasm resources, molecular markers and innovative lines for breeding new salt-tolerant rice varieties.