Field investigations were carried out at the Experimental Farm, Rice Research and Training Center, Field Crops Institute, and ARC during the growing seasons 2021 and 2022 to study the effect of cytokinin and molybdenum on hybrid seed production. The experiments comprised four treatments, viz., T1 (control), T2 (cytokinin) with a 20 ppm concentration, T3 (molybdenum) with a 35 ppm concentration, and T4 (a 1:1 mixture of cytokinin 10 ppm and molybdenum 17.5 ppm) as a pre-flowering treatment for male parent Giza 178 R and female parent for five Cytoplasmic Male Sterility (CMS) lines (IR69625, IR70368, IR58025, K17, and G46) on hybrid rice seed production. The treatments were conducted. The CMS lines were arranged in the main plots, while treatment applications were distributed in subplots and three replications. The exogenous application of treatments such as cytokinin and molybdenum could improve the crossing rates of the male parent by affecting floral traits and, accordingly, increase hybrid rice seed production. The most significant effects of treatment on anther length, anther width, pollen fertility, number fertility, stigma width, stigma length, days to heading, number of fertile tiller hills-1, plant height, panicle length, seed set, and grain yield of male parent Giza 178R were (T4), a combination between cytokinin and molybdenum. Duration of floret opining, total stigma length, stigma length, angle of floret opining, stigma width, stigma burch, days to heading, plant height, number of fertile panicles hill-1, flag leaf angle, panicle exertion, panicle length, panicle mass, seed set, seed yield, and harvest index of CMS lines were significantly affected by treatments. Moreover, the evaluated CMS lines exhibited significant differences in all measured floral traits. Line 2, Line 3, and Line 1 displayed the uppermost spikelet opening angle, duration of spikelet opening, total stigma length, style length, stigma brush, and stigma width. In addition, these CMS lines exhibited the highest plant growth and yield traits, particularly under T4. Consequently, exogenous application of T4 in combination with cytokinin and molybdenum could be exploited to improve the floral, growth, and yield traits of promising CMS lines such as Line 1, Line 3, and Line 4, thereby increasing outcrossing rates and hybrid rice seed production.