Cotton is a moderately salt-tolerant crop, but its salt tolerance threshold is not more than 7.7 ds•m−1. The seedling stage of cotton is the highly sensitive to salinity and the effects can be quantified by measuring morphological and physiological traits. The purpose of this study was to identify QTLs related with salinity tolerance at seedling stage. Meanwhile where they were localized in the genome, investigate the relationships between the traits at seedling stage under salt and to find candidate genes related with salt tolerance. To achieve this goal, two upland cotton accessions mainly cultivated in China; CCRI-35 (Source: 132062) tolerant to salinity as female parent and Nan Dan Ba Di Da Hua: NH (Source: 130549) sensitive to salinity as male parent and their 277 offspring F2:3 population have been used. Our experiment revealed 05 consistent QTLs found in at least two environments. Only 02 major QTLs with high phenotypic variation explained by a single QTL, R2 (%), and high percentage of heritability, HB (%), values were detected on chromosome Chr1 and Chr 7/ Chr16.These QTLs explained phenotypic variation from 5.7 to 60.03 %. Broad sense heritability was high for SL (83.1%) and moderate for GR (68.4). These 02 major QTLs and the 26 genes identified in this study could be used in cotton breeding program and with few obstacles.