Carotenoids are not naturally accumulated in the endosperms of rice, which is a cereal crop. In our previous study, biofortifed rice seeds accumulated two red color carotenoids, ketocarotenoids including astaxanthin and ketoxanthophylls including capsanthin, via four-step pathway engineering. Their biosynthetic pathways require zeaxanthin as a common precursor and then bifurcated. In this study, cross-fertilization between two astaxanthin (BP and sBP) and two capsanthin (C and CB) rice plants were reciprocally performed to elucidate the rice seed system’s metabolic preference. Filial seeds showed diferent colors in red hues between mutually interbred lines as well as from parents. The strongest driving force for metabolism was caused by the sBP line for astaxanthin regardless of the parent side and proved to be the most efcacious customized synthetic gene for rice crops. It further resulted in the highest astaxanthin levels when paternal sBP mated with maternal CB line, which has the biggest capacity of total carotenoids. Also, reciprocal crosses between CB and BP lines ascertained their metabolically balanced gene efcacy by showing the pathway preference toward either ketoxanthophylls or ketocarotenoids depending on the paternal parental side. Our study suggests that gene efcacy plays the most decisive role in leading the metabolic path and revealed the unexpectedly paternal parent-of-origin efects in the endosperm. Consequently, we simultaneously biofortifed rice crops with two functional red carotenoids and fnally generated new red-colored