Developing high-yielding rice genotypes is decisive to ensure global food security with current population growth and threat of environmental pressures. Cytoplasmic male sterility (CMS) system provides a valuable approach for commercial exploitation of heterosis and producing high-yielding and quality hybrid rice. Three CMS lines and ten diverse restorers were crossed using line × tester mating design. The obtained thirty F1 hybrids and their thirteen parents were evaluated. Yield traits as well as certain floral traits characters that influence the efficiency of crossing and hybrid seed production as duration of floret opening (min), stigma exsertion (mm), stigma length (mm), opening floret angle, and anther length (mm) were assessed. Highly significant variations were detected among parents, crosses, and parents vs. crosses for all the studied traits. The CMS line L2 and the restorer T5 were determined as good combiners for stigma exsertion, stigma length, opining floret angle, and duration of floret opening. Besides, the hybrids L1×T1, L1×T3, L2×T2, L2×T5, L3×T4, L3×T5, and L3×T9 exhibited positive SCA effects for most floral traits. Moreover, the CMS lines L1 and L3 as well as the restorers T1, T2, T3, T6, and T9 were identified as good general combiners for grain yield and certain related traits. The hybrids L1×T1, L1×T5, L1×T7, L2×T3, L2×T4, L2×T5, L2×T10, L3×T1, L3×T2, and L3×T6 displayed positive SCA effects for grain yield and one or more of its attributes. Both additive and non-additive gene effects are involved in the governing inheritance of all evaluated traits. The biochemical variations among the certain evaluated genotypes were further studied. The esterase and peroxidase isozymes were applied for verifying the genetic diversity at the protein level among the used CMS lines, restorers, and their crosses. All the applied isozymes displayed polymorphism for the parents and their crosses. The banding pattern and intensity differences provided accurate results on the reliable variability among the tested genotypes.