Common wheat (Triticum aestivum L.) is one of the most important and strategic staple food crops for majority of the world’s population. Despite the fact that wheat breeding has significantly contributed to increasing the yield potential, terminal heat stress significantly affected flowering, grain filling and ultimately grain yield in wheat. Our objective was to identify quantitative trait locus (QTL) linked to morphological, physiological, developmental and yield and yield-component traits under heat stress in wheat. A set of 177 doubled haploid (DH) lines derived from a cross between two diverse cultivars PBW343 (heat sensitive) and Giza168 (heat tolerant parent) was used. The parents and the DH lines were evaluated for 18 traits under three planting dates viz., timely sown (non-stress), late sown (moderate heat stress) and very late sown (severe heat stress) at two locations (Meerut and Lucknow) for three consecutive crop seasons (2018, 2019, and 2020). Parents and DH lines were genotyped using genotyping-by-sequencing (GBS) approach, which identified 26,213 polymorphic SNP markers. Markers with >20% missing values and incorrectly genotyped by not following parental alleles were removed from the dataset, as a result 5,710 high-quality SNP markers were physically mapped on 21 wheat chromosomes covering a total physical length of 13,908.2 mega base pair (Mbp). Quantitative trait loci (QTLs) analyses were carried out using composite interval mapping (CIM) method in QTL Cartographer v2.5. QTL analysis of pooled data detected 70 significant QTLs belonging to all the 18 traits. These QTLs were distributed on all the wheat chromosomes except chromosome 4B. Maximum QTLs were associated with days to heading and harvest index. Average LOD scores of these QTLs ranged from 2.50 to 9.43 (3.64) and explained up to 40% of the phenotypic variation. Identified QTLs will be useful for breeders to improve terminal heat stress in wheat.