This work represents MeSCoT, a software dedicated to complex trait simulation through the mechanistic modelling of genes interactions. The software provides an innovative framework to study molecular mechanisms of gene-by-gene and gene-by-environment interactions. It closely imitates the basic in vivo mechanisms of complex trait realization and allows a detailed simulation of genes' regulatory interactions for variable genomic architectures. The MeSCoT software is scalable and well documented (https://genetics.ghpc.au.dk/vimi/mescot/).