Hybrid rice breeding is the combining ability breeding. Screening hybrid rice combinations with high special combining ability (SCA) is able to breed strong superiority combinations with practical values. In this study, the genetic distances (GD) of nine three-line hybrid rice (5 CMS lines and 4 restorer lines) were examined using SSR markers. Based on yield performances of 20 hybrid crosses (5×4 NCII), the relationships between SCA, heterosis and GD were studied. The correlations of yield SCA with the control heterosis (r₁=0.5609) and the average heterosis (r₂=0.541) were significant, but not significant with GD (r=0.2143). Thus, the heterosis can be reflected by SCA; the hybrid parents selected in this study can be used to develop strong superiority combinations; but the SCA cannot be reflected by GD, which needs further study.