Eight male sterile lines and ten restorer lines of hybrid rice in South China were crossed to develop two half-diallel mating sets designed according to NCII and sixty-one F1s were obtained. These F1s were planted in 2005 and 2006 respectively, and the combining ability for yield traits in its eighteen parents were evaluated and screened by sixty-two SSR markers related to functional QTLs. The results showed that there were obvious differences in general combining ability among these parent lines, and four parent lines including Zhenshan97A, WanjinA, Zhilong and Guanghui3550 had elite general combining ability. There were thirty-six SSR molecular locus associated with combining ability of yield traits, and marker locus RM1, RM216, RM231 and RM542 were detected in two sets of materials. Among them, twenty-three were effect-increasing locus while others were effect-decreasing locus. Heterozygous locus of RM231 and RM209 were two marker locus of elite combining ability for yield with the maximum increasing effects, which increased 13.50% and 16.43% of yield in F1, respectively. The results could be directly used for yield improvement and choice of parents for developing hybrid rice in South China.