Plant hormone cytokinin signals through histidine-aspartic acid (H-D) phosphorelay to regulate plant growth and development. Whilst it’s well-known that the phosphorelay involves histidine kinases, histidine phosphotransfer proteins (HPs) and responsive regulators (RRs), how this process is regulated by external components remains unknown. Here we demonstrate that PPKL1 (Protein Phosphatase with Kelch-Like domains), known as a signaling component of steroid hormone brassinosteroid, is actually a cryptic inhibitor of cytokinin phosphorelay in rice (Oryza sativa L.). Mutation at a specific amino acid D364 of PPKL1 activates cytokinin response, thus enlarges grain size in a semi-dominant mutant named s48. Overexpression of PPKL1 containing D364, either with the deletion of the phosphatase domain or not, rescues the s48 mutant phenotype. PPKL1 interacts with OsAHP2, one of authentic HPs, and D364 resides in a region resembling the receiver domain of RRs. Accordingly, PPKL1 can utilize D364 to suppress OsAHP2-to-RR phosphorelay, whereas mutation of D364 abolishes the effect. This function is independent of the phosphatase domain that should be required for brassinosteroid signaling. Importantly, editing of the D364-residential region produces a diversity of semi-dominant mutations associated with variously increased grain sizes. Screening of them enables the identification of two genotypes conferring significantly improved grain yield. We therefore uncover a noncanonical cytokinin signaling suppressor and a robust tool for seed rational design.