Chromosomal segment introgression or substitution lines (CSILs or CSSLs) are defined as a set of lines each of which contains only one or few chromosomal segment from the donor and genetic background of each line is similar to receptor. Compared with the traditional mapping populations, the CSILs might have an advantage for identifying of quantitative trait locus (QTL) due to eliminating of residual background which can lead to decrease power of QTL detecting. Therefore, population of CSILs is one of the ideal materials for QTL identifying and fine mapping, assay of QTL interaction and QTL × environment interaction, as well as for heterosis utilization and QTL pyramiding. In this paper, the advanced progresses on the construction and application of CSIL population in crop plants were reviewed.