Durum wheat (Triticum turgidum ssp. durum), which constitutes the raw material of pasta, is the 10th most important cereal worldwide. A key goal in order to meet its upcoming demand while coping with climate change, is to understand the genetic control behind thousand kernel weight (TKW), a major component of grain-yield. A strategy to achieve this is to explore new genetic resources as domesticated emmer (T. turgidum ssp. dicoccum) to discover favorable alleles that affect kernel morphological factors, which have a determining role on TKW. Therefore, the present study aimed to explore the genetic network responsible for kernel size components (length, width, perimeter and area) and kernel shape (width-length ratio and form coefficient) and their relationships with kernel weight and heading date. QTL mapping was performed on a segregating population of 110 recombinant inbred lines, derived from a cross between T. dicoccum accession MG5323 x T. durum cv. Latino, evaluated in 4 different environments. A total of 20 QTL were found environmentally stable and further grouped in 6 clusters on chromosomes 2B, 3A, 3B, 4B, 6B and 7A. Among them, a QTL cluster on 4B chromosome was associated with kernel size traits and TKW, where the parental MG5323 contributed the favorable allele, highlighting its potential to improve durum wheat germplasm. Further, the physical positions of the clusters, defined by the projection on the T. durum reference genome, overlapped with already known genes, such as BIG GRAIN PROTEIN 1 on chromosome 4B. These results might provide genome-based guidance for the efficient exploitation of T. dicoccum variability in wheat, possibly through yield-related molecular markers.