Hybrid seed set on the female line depends on its flowering synchronization with the restorer line (R), therefore, the sowing of male and female lines must be planned properly. During 2016 and 2017 summer seasons, a preliminary investigation was carried out to study the leaves number, days to heading and effective accumulated temperature as principle methods to determine the synchronization of the CMS line and the restorer line. Besides, an experiment was carried out during 2018 and 2019 to investigate the effect of synchronization method on flowering synchronization on hybrid rice seed production. Results indicated that the method of flowering synchronization between CMS lines and R lines had highly significant effects on the traits: panicle weight, seed set percentage, harvest index and seed yield of hybrid rice. The highest seed yields were 1.760 and 1.870 t ha−1. They were recorded from the number of leaves method and the hybrid combination of Giza 178R × IR69625A, respectively. The number of leaves is the best time for the synchronization of hybrid rice lines and the hybrid combination Giza 178R × IR69625A may be recommended for better performance. It was noticed that planting restorer line rows at three different dates with four times of supplemental pollination resulted in the highest number of fertile panicles hill-1, panicle weight, number of filled grains panicle-1 and hybrid seed yield.