In order to mine elite alleles of panicle traits in rice, a population of chromosome segment substitution lines (CSSLs) was constructed by using an indica variety II-32B as receptor parent and a japonica variety A7444 as donor parent. QTLs for seven panicle traits were detected using the CSSL population by QTL IciMapping 4.1 software. A total of 26 QTLs for the seven traits were identified across two years. Among the 13 QTLs detected in both years, four QTLs for primary branch number (PBN) were located on chromosomes 1, 6, 8, and 9, with average contribution rate of 15.16%, 13.1%, 29.74%, and 11.21%, and average additive effects in two years of ?1.40, 1.01, 1.11, and 0.77, respectively. Two QTLs for secondary branch number (SBN) were located on chromosomes 6 and 8, with average contribution rate of 10.97% and 21.39%, and average additive effects of 5.45 and 6.36, respectively. Three QTLs for spikelets per panicle (SPP) were located on chromosomes 2, 6, and 8, with average contribution rate of 8.65%, 12.52%, and 31.22%, and average additive effects of ?18.61, 22.23, and 31.87, respectively. One QTL for grains per panicle (GPP) was located on chromosome 8, with average contribution rate of 28.06%, and average additive effect of 30.85. Two QTLs for 1000-grain weight (TGW) were located on chromosome 2, with average contribution rate of 44.65% and 17.51%, and average additive effects of 2.88 and ?2.51. One QTL for grain width (GW) was located on chromosome 10, with average contribution rate of 21.96% in two years, and average additive effect of 0.11. QTL segment controlling SBN, SPP and GPP simultaneously were found on chromosomes 2, 6 and 8, respectively. From the bi-parent DNA sequence comparison, it is speculated that QTL qSBN6 and qSBN8 might be different alleles of Hd1 and DTH8, respectively. QTL qSBN2 was a novel locus detected in the present study. The results of this study provide useful information for pyramiding breeding through marker-assisted selection.