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Neodiosmin has poor aqueous solubility but exerts a good debittering effect and is a strong antioxidant with potential applications in foods, beverages, and pharmaceutical preparations. The water solubility of neodiosmin was greatly enhanced by forming a neodiosmin/β‐cyclodextrin/lysine ternary inclusion complex. The inclusion type is described in detail in terms of its structural aspects using a phase diagram of solubility. The neodiosmin/β‐cyclodextrin/lysine ternary inclusion complex was synthesized and characterized by thermal analysis and powder X‐ray diffractometry (XRD). The molecular and fractal structures of the ternary complexes were investigated using 1H nuclear magnetic resonance (1H NMR) spectroscopy and Fourier transform infrared (FT‐IR) spectroscopy. Additionally, scanning electron microscopy (SEM) revealed that neodiosmin was embedded in a matrix of β‐cyclodextrin with lysine. The results demonstrated that the inclusion complex was formed and that the solubility of neodiosmin was greatly improved. Additionally, the bitterness‐masking power of this system was evaluated by a panel test using a series of limonin concentrations as a reference scale. The neodiosmin/β‐cyclodextrin/lysine ternary inclusion complex showed the highest efficacy, and the bitterness attenuation was statistically significant.