Rice, the major crop sustaining approximately half the world population, has been extensively reported to be sensitive to saline conditions. However, the genetic and physiological understanding related to long-term salinity stress remains unclear so far. The aim of this study was to evaluate the mechanisms of salinity tolerance in a salinity-tolerant variety of rice, Nona Bokra, and to detect the chromosomal regions responsible for it. We utilized chromosome segment substitution lines (CSSLs) carrying segments from Nona Bokra in the genetic background of a salt-sensitive variety Koshihikari by investigating the plant growth, grain productivity, and ion contents in plants subjected to long-term salinity stress. Comparison of plant growth and grain yield of CSSLs grown under long-term saline conditions suggests that the salinity tolerance of Nona Bokra involves the improvement of plant dry matter, panicle number, and percentage of ripened grains. Nona Bokra has the chromosomal regions for the improvement of the panicle number on chromosome 2 and the percentage of ripened grains on chromosome 6 or 10 under salinity conditions. It was suggested that these chromosomal regions were related to Na+ and Cl- exclusion. Low Na+ and Cl- contents in whole plant at full heading stage would be vital for improving the yield under long-term saline conditions.