To provide theoretical reference for breeding high-yield and high light utilization efficiency of hybrid rice, the combining ability and genetic characteristics of chlorophyll fluorescence of flag leaves were researched. Thirty different hybrid rice combinations from incomplete diallel crosses (between six sterile lines and five restorer lines of indcia hybrid rice cultivars) were tested. Result showed that there were significant genetic differences(P＜0.01) for chlorophyll fluorescence parameters among the hybrid rice combinations. Fm, ΦPSII and ΦNPQ in hybrid rice combinations were affected by gene additive effects and non-additive effects but other chlorophyll fluorescence parameters (Fo, Fv/Fm, ΦNO, NPQ, qL) mainly affected by non-additive effects. The proportion of female parent GCA variance was much bigger than the proportion of male parent GCA variance of ΦPSII and ΦNPQ, indicating that the chlorophyll fluorescence parameters of hybrid rice combinations were more affected by the sterile lines than restorer lines. The broad-sense heritability was greater than the narrow-sense heritability in chlorophyll fluorescence parameters of indica hybrid rice combinations. Four chlorophyll fluorescence parameters such as Fm, ΦPSII, ΦNPQ, and NPQ with the narrow-sense heritability from 20% to 50% had moderate heritability. The others chlorophyll fluorescence parameters (Fo, Fv/Fm, ΦNO, qL) with narrow-sense heritability below 20% had weak heritability. The competitive advantage of hybrid rice combinations for ΦPSII was positively correlated with female GCA (P<0.01) and with a higher determination coefficient, indicating that the hybrid rice combinations from female parents with higher GCA have higher competitive advantages. Selecting sterile lines with excellent combining ability and phenotypic value of ΦPSII was the key step while selecting good restorer lines can not be ignored during breeding hybrid rice combinations of high light utilization efficiency.