Hybrid rice has achieved high grain yield and greatly contributes to food security, but manual labor-intensive hybrid seed production process limits fully mechanized hybrid rice breeding. For next-generation hybrid seed production, it is promising to utilize small grain male sterile lines to mechanically separate small hybrid seeds from mixed harvest. However, it is difficult to find ideal grain size genes for breeding ideal small grain male sterile lines without penalties in the number of hybrid seeds and hybrid rice yield. Here we report that the utilization of small grain alleles of the ideal grain size gene GSE3 in male sterile lines enables fully mechanized hybrid seed production and dramatically increases hybrid seed number in three-line and two-line hybrid rice systems. The GSE3 gene encodes a histone acetyltransferase that binds histones and influences histone acetylation levels. GSE3 is recruited by the transcription factor GS2 to the promoters of their co-regulated grain size genes and influences the histone acetylation status of their co-regulated genes. Field trials demonstrate that genome editing of GSE3 can be used to immediately improve current elite male sterile lines of hybrid rice for fully mechanized hybrid rice breeding, providing a new perspective for mechanized hybrid breeding in other crops.