Salt stress is an important abiotic stress, which has seriously affected the reproductive development of rice in many parts of the world. Therefore, it is particularly important to understand the genetic mechanism of salt tolerance in rice. In this study, we preliminarily located some quantitative trait loci (QTL) for root length, bud length, and survival percent under different salinity conditions (0, 100, 200 and 400 mM NaCl), using a population of chromosome segment substitution lines (CSSLs) constructed by Nipponbare and 9311. A total of 20 QTLs were identified, which explained the phenotypic variation of 4.7636%~37.5870%. There are 7, 5 and 8 QTLs for root length, bud length and survival percent, respectively. And qRL1, qSP2, qSP3, qSP4, qRL5, qSP7, qSP7-1, qSP9, qRL10, qRL10-1, qRL11, qRL11-2, qBL11, qBL11-1 and qSP12 were reported for the first time. Under different salinity conditions, the QTLs located are different, that is to say, the salt tolerance mechanism of rice under different salinity conditions may be different. The specific genetic mechanism remains to be further verified. Those QTLs identified in the experiment may be valuable genetic factors for improving salt tolerance of rice. These QTLs can be used to improve salt tolerance of rice by molecular markers technology, which will help to further understand the genetic mechanism of salt tolerance of rice.