A histone deacetylase gene OsHDT1 which enhances utilization of heterosis in rice is isolated and cloned, said gene consisting of: 1) the DNA sequence of positions 1-894 in SEQ ID NO:1 in the Sequence listing; or 2) a DNA sequence which encodes the same protein as that encoded by the DNA sequence of 1). The histone deacetylase gene OsHDT1 is associated with enhanced utilization of heterosis in rice. When the transgenic plants having no phenotype were crossed with “Zhenshan 97A”, the F1 overexpression hybrid plants have obviously earlier flowering period than F1 wild-type hybrid plants. Moreover, the RNAi inhibition hybrid plants have a decreased seed setting rate compared to the negative control hybrid plants, while the parent RNAi inhibition plants and negative control plants shows no evident difference in the trait of seed setting rate. Western blotting revealed that the gene is capable of deacetylating histone, mainly at H4K16 site. In addition, there exist significant differences in the level of histone modification among “Minghui 63”, “Zhenshan 97” and “Shanyou63”.