In this study, QTLs of heading date (HD) and purple trait were identified using a chromosomal segments substitution line population which wild rice as donor parent and 9311 as receptor parent. Days of heading of CSSLs were investigated from multi-environments, eleven HD QTLs were identified using more than 200 molecular makers. Two CSSLs which significantly heading later under long day condition were selected for HD gene mapping, and two previously reported flowering time genes were found. One CSSL, which have significant purple trait was selected for purple trait gene mapping, an OrC gene, associated with anthocyanin biosynthesis was identified. We found that OrC gene have different function with cultivated rice allele. Our data indicated that the CSSLs population was an efficient genetic material for wild rice gene mapping. Those genes provided new gene resources for rice breeding and new evidences for rice domestication study.