Tillering is a major determinant of rice plant architecture and grain yield. Here we report that depletion of rice OsNRPD1a and OsNRPD1b, two orthologues of the largest subunit of RNA polymerase IV, leads to a high-tillering phenotype, in addition to dwarfism and smaller panicles. OsNRPD1a and OsNRPD1b are required for the production of 24-nt siRNAs that direct DNA methylation at transposable elements (TEs) including Miniature Inverted-repeat TEs (MITEs). Interestingly, many genes are regulated either positively or negatively by TE methylation. Among them, OsMIR156d and OsMIR156j, which promote rice tillering, are repressed by CHH methylation at two MITEs in the promoters. By contrast, D14, which suppresses rice tillering, is activated by CHH methylation at a MITE in its downstream. Our findings reveal control of rice tillering by RdDM at MITEs and provide potential targets for agronomic trait enhancement by epigenome editing.