Plant height is an important agronomic trait. Dramatic increase in wheat yield during the “green revolution” is mainly due to the widespread utilization of the Reduced height (Rht)-1 gene. We analyzed the natural allelic variations of three homoeologous loci Rht-A1, Rht-B1, and Rht-D1 in Chinese wheat (Triticum aestivum L.) micro-core collections and the Rht-B1/D1 genotypes in over 1,500 bred cultivars and germplasms using a modified EcoTILLING. We identified six new Rht-A1 allelic variations (Rht-A1b-g), eight new Rht-B1 allelic variations (Rht-B1h-o), and six new Rht-D1 allelic variations (Rht-D1e-j). These allelic variations contain single nucleotide polymorphisms (SNPs) or small insertions and deletions in the coding or uncoding regions, involving two frame-shift mutations and 15 missenses. Of which, Rht-D1e and Rht-D1h resulted in the loss of interactions of GID1-DELLA-GID2, Rht-B1i could increase plant height. We found that the Rht-B1h contains the same SNPs and 197 bp fragment insertion as reported in Rht-B1c. Further detection of Rht-B1h in Tibet wheat germplasms and wheat relatives indicated that Rht-B1c may originate from Rht-B1h. These results suggest rich genetic diversity at the Rht-1 loci and provide new resources for wheat breeding.