Multidrug and toxic compound extrusion proteins (MATE) can transport small organic molecules in and out of cells and participate in detoxification, nutrient absorption, disease resistance and plant development processes. These compounds are widely distributed in plants. However, the mechanism by which MATE affects grain development remains elusive. In this study, we studied a MATE transporter, OsMATE2, which localized on the membrane. The CRISPR-Cas9 (CR) knockout line of OsMATE2 presented obvious decreases in grain weight. In addition, root development was also affected. Two proteins that interact with OsMATE2, namely, manganese-superoxide dismutase (Mn-SOD) and poly(A)-binding protein (PABP), were identified from a screening of yeast library. The results were validated through yeast two-hybrid and bimolecular fluorescence complementation experiments. The CRISPR-Cas9 (CR) knockout lines of Mn-SOD and PABP presented increased grain size and weight. Our findings demonstrated that OsMATE2 interacts with Mn-SOD and PABP to regulate grain development in rice.