Plant height is the important determinant for the yield formation of rice, and selecting of an optimal plant height is necessary during rice breeding to achieve ideal biomass and lodging resistance. In this study, allele variation of Sd1, the well-known “green revolution” gene, was clarified as the major factor for plant height segregation in the breeding populations from an indica and japonica cross. Two null sd1 alleles (sd1^N1, sd1^N2) and two functional Sd1 alleles (Sd1^Jap and Sd1^Ind) were characterized by newly developed functional markers, which demonstrated high efficiency for genotyping a large set of germplasms. We found that the null alleles, which were enriched in the modern indica but not japonica varieties in China, presented universal effects to shorten plant height despite the genetic backgrounds and environments. The effect of the Sd1^Jap allele for plant height was weaker than that of Sd1^Ind but sensitive to the genetic background of different subspecies, suggesting complex epistatic interactions between Sd1^Jap and other plant height loci. In addition, Sd1^Jap was identified to be compatible with some hybrid varieties recently developed in China, raising its potential value for hybrid rice breeding. Finally, we carried out a breeding practice by introgressing the null sd1 allele into the elite japonica variety Daohuaxiang, which suffers from severe lodging, and clarified the agronomic performance of the improved semi-dwarf line. This study will pave the way for the effective application of different Sd1 alleles in both inbred and hybrid breeding in the future.