Precise regulation of cell proliferation and differentiation is vital for organ morphology. Rice palea, serving as sepal, comprises two distinct regions: the marginal region (MRP) and body of palea (BOP), housing heterogeneous cell populations, which makes it an ideal system for studying organ morphogenesis. We report that the transcription factor (TF) REP1 promotes epidermal cell proliferation and differentiation inthe BOP,resulting in hard silicified protrusion cells, by regulating the cyclin-dependent kinase gene, OsCDKB1;1. Conversely, TFs OsMADS6 and OsMADS32 are expressed exclusively in the MRP, where they limit celldivision rates by inhibiting OsCDKB2;1 expression and promote endoreduplication, yielding elongatedepidermal cells. Furthermore, reciprocal inhibition between the OsMADS6-OsMADS32 complex andREP1 fine-tunes the balance between cell division and differentiation during palea morphogenesis. Wefurther show the functional conservation of these organ identity genes in heterogeneous cell growthin Arabidopsis, emphasizing a critical framework for controlling cellular heterogeneity in organ morphogenesis.