Size scaling describes the relative growth rates of different body parts of an organism following a positive correlation. The genetic mechanism of the size scaling and how artificial selection influencing the pattern of size scaling remain unexplored. Here we utilise diverse barley panel with genome-wide single nucleotide polymorphisms (SNPs) and the measurement of their plant height and seeds weight to explore the genetic mechanisms that lead to a correlation of the two traits and the influence of domestication and breeding selection on the size scaling. Plant height and seeds weight are heritable and remain positively correlated in domesticated barley regardless of growth type and habit. Genome-wide association studies revealed eight SNPs to be associated with both traits. Linkage decay analysis suggests that a considerable proportion of genetic markers associated with either plant height or seeds weight are closely linked in the chromosome. Common factor analysis revealed twenty SNPs conferring pleiotropic effect on both traits. Genes with multiple functions in plant growth and development are involved in structuring plant height and seeds weight scaling. Pleiotropy forms the genetic bases of plant height and seeds weight scaling in barley. Our results suggest an alternative hypothesis for seeds weight evolution in domestication that the selection in plant size may have constrained variation in seeds weight. Our findings contribute to the understanding of the genetic basis of size scaling and open a new venue for seeking the underlying mechanism of a grand theory on allometric scaling in plants.