Post-translational modifications of nucleosomal core histones play important roles in biological processes via altering chromatin structure and creating target sites for proteins acting on chromatin. Molecular genetic studies with Arabidopsis have verified several epigenetic factors that regulate flowering time. However, the roles of chromatin remodeling factors have not been well explored in rice. Here, we identified chromatin remodeling factors, OsVIL1, 2, and 4 (Oryza sativa VIN3-LIKE) genes, that regulate grain yield. OsVIL proteins contain a plant homeodomain (PHD) finger, which is a conserved motif of histone binding proteins. We showed that plant height and number of spikelets per panicle were increased in the OsVIL2-overexpression (OsVIL2-OX) and osvil4 plants, respectively. Each mutants (OsVIL2-OX and osvil4) exhibited longer internodes and thicker stems than wild type controls. Histochemical analysis revealed that cells are smaller in OsVIL2-OX and osvil4 plants. We performed an RNA-seq using 1st internodes of WT and OsVIL2-OX stems and got the suppressed target genes in the OsVIL2-OX. OsCKX2, which encodes cytokinin oxidase/dehydrogenase is one of the suppressed genes in the OX plants and we verified decrease of that gene using qRT-PCR and closed chromatins of OsCKX2 were enriched in the OX plants by using ChIP. As results of these, cytokinins were enriched in the OX plants. These demonstrate that OsVIL2 and OsVIL4 antagonistically regulate plant height and number of spikelets by controlling cytokinin contents. Like OsVIL2-OX and osvil4 plants, besides, OsVIL1-OX plants were also shown increased plant height and biomass. We propose that OsVILs may be used for improving grain yield by increasing biomass.