Pomegranate (Punica granatum) has staminate (male), androgynous (hermaphrodite), and intermediate flower types. Floral characterization is difficult for breeding efficiency across many pomegranate genotypes in Pakistan, which is essential for pomegranate cultivar enhancements. The present research focused on the floral characterization and breeding efficiency of fifteen pomegranate genotypes. Flower sex ratio, floral morphological parameters, i.e., flower length, ovary width, flower notch, flower tip and stigma with style length, and fruit set percentage were examined during the experiment. In terms of sex ratio, male flowers were found to be higher among all genotypes. Due to clear differences in flower length, width, and heterostyly facilitating visual identification of the hermaphrodite flowers, genotype Ternab-2, Kandhari White, and Kandhari Red had higher fruit set (≥70%) among all cross combinations attempted. Genotype Sava had higher flower length and heterostyly of hermaphrodite flower type, but ovary width was not very distinct, leading to average crossing success (85–34%). In conclusion, single or combination of morphological characters can be used for accurate identification of hermaphrodite flowers, which can improve hybrid efficiency and fruit set after artificial cross-pollination.