Nitrate is an important nutrient and a key signaling molecule for plant development. A number of transcription factors involved in the process of nitrate response and their regulatory mechanisms have been identified. However, little is known about the nitrate sensor transcription factors and their regulatory mechanisms among crop plants. In this study, we identified functions of a nitrate-responsive miR444:MADS-box transcription factor OsMADS27 module and its downstream targets mediating rice root growth and stress responses. Transgenic rice plants expressing miR444 target mimic improved rice root growth. Although miR444 has the potential to target multiple genes, we identified OsMADS27 as the major miR444 target that regulates the expression of nitrate transporters, as well as several key genes including expansins and those associated with auxin signaling promote root growth. In agreement with this, overexpression of miRNA-resistant OsMADS27 improved root development and tolerance to stresses, while its silencing suppressed root growth. OsMADS27-mediated a robust stress tolerance in plants through its ability to bind to the promoters of specific stress regulators as observed in ChIP-Seq analysis. Our results provide evidence of nitrate-dependent miR444-OsMADS27 signaling cascade involved in the regulation of rice root growth as well as its surprising role in stress responses.