Capparis masaikai Lévl is a Chinese native plant that ripe seeds are often used as a traditional Chinese medicine for their heat antidotes properties. The locals like to chew the seeds for their distinctive flavor “sweet water taste”. In this study, enzymatic hydrolysis, gel filtration chromatography, and reversed-phase high-performance liquid chromatography were used to extract, isolate and purify flavor peptides from the seed kernels of Capparis masaikai Lévl. Nano-LC−MS/MS was used to identify 219 peptides in total. Five new bitter peptides (HIGP, FHP, CFR, LYR and SFR) were screened by molecular docking. The results of molecular docking indicated that hydrogen bonds and hydrophobic bonds played essential roles in the binding of the five bitter peptides to T1R2-T1R3, T2R1 and T2R34. Phe75 and Glu74 on T2R1 and Arg373 on T1R2-T1R3 might be the critical amino acids in the binding site. The taste properties of the synthesized peptides were confirmed by sensory evaluation, and it was found that five peptides exhibited a specific sweetness inhibition. Not only do these results shed light on the interaction between flavor peptides and taste receptors, but they also help explain the “sweet water taste” of the seed kernels of Capparis masaikai Lévl. The results of this study help to explore the potential of flavor peptides in an enzymatic hydrolysate of Capparis masaikai Lévl seed kernels and broaden the diversity of flavor sources for the “sweet water taste”.