qPh-3D is a major quantitative trait locus （QTL） regulating plant height （PH） in wheat. This locus could be repeatedly identified in datasets at 14 different environments in the recombinant inbred line （RIL） population derived from the cross between Kenong 9204 and Jing 411 （denoted as KJ-RILs）. qPh-3D was mapped to the chromosomal region of KN3D：515.08-539.08 Mb， and the allele from parent Jing 411 could reduce PH. In this study， we aimed to further characterize the genetic mechanism of PH reduction caused by qPh-3D and clarify its genetic effects on yield-related traits， using the KJ-RILs population containing 187 lines as well as a natural mapping population consisting of 316 breeding varieties （advanced lines）. In KJ-RILs， the qPh-3D allele from Jing 411 can significantly reduce PH via reducing all internode lengths without significant effect on spike length （SL）， whereas it can reduce kernel yield per plant （KYPP） at certain level. Two markers AX-110160363 and AX-111109273， which closely link with qPh-3D， were used for genotyping in the natural mapping population with the yield-related phenotypic datasets. The qPh-3D allele with decreased PH was found with a positive effect on SL， but a significant negative effect on KYPP. Based on the breeding selection effect analysis at the qPh-3D locus， the qPh-3D allele with decreased PH was present in a higher proportion in wheat varieties released from Beijing and Shanxi in China， but lower in Shandong， Qinghai， Sichuan and the foreign countries. This allele was detected in a lower proportion in earlier varieties， while its presence in modern varieties was detected increasingly. In addition， a closely linked PCR-based InDel marker targeting the qPh-3D locus was developed. Collectively， the findings of this study will provide theoretical guidance for future applications of qPh-3D in molecular breeding programs in wheat.