Floral colour polymorphism occurs in many species throughout the angiosperms but the mechanisms of selection remain unclear. In this study, we studied the pollen–pistil interactions between different Butomus umbellatus plants, a clonal aquatic plant with red and white-flowered individuals. Results indicated that red-flowered plants have lower asexual and sexual reproductive output compared to white-flowered plants in monomorphic populations, even though there are no differences in flower characteristics and pollination systems. On the other hand, in polymorphic populations, sexual reproductive output in red-flowered plants increases while asexual reproductive output decreases considerably. However, this remains unaffected in white-flowered plants. Artificial pollination treatments revealed asymmetric pollen–pistil interactions between red and white-flowered individuals. Inter-morph crosses increase seed production only when the red-flowered plant is maternal. Moreover, pollen grains of white-flowered plants significantly enhance not only female fitness by way of greater seed yields, but also male fitness by promoting fertility of pollen on stigma within a flower. Such special pollen–pistil interactions might form one kind of balancing selection and actively maintain both genotypes of the two morphs. These findings may enrich our understanding of mechanisms of maintaining plant reproductive polymorphism.