Grain boundary (GB) segregation is an important phenomenon that affects many physical properties, as well as microstructure of polycrystals. The segregation of solute atoms on GBs and its effect on GB structure in Al were investigated using two approaches: First principles total energy calculations and the finite temperature large-scale atomistic modeling within hybrid MD/MC approach comprising molecular dynamics and Monte Carlo simulations. We show that the character of chemical bonding is essential in the solute–GB interaction, and that formation of directed quasi-covalent bonds between Si and Zn solutes and neighboring Al atoms causes a significant reconstruction of the GB structure involving a GB shear-migration coupling. For the solutes that are acceptors of electrons in the Al matrix and have a bigger atomic size (such as Mg), the preferred position is determined by the presence of extra volume at the GB and/or reduced number of the nearest neighbors; in this case, the symmetric GB keeps its structure. By using MD/MC approach, we found that GBs undergo significant structural reconstruction during segregation, which can involve the formation of single- or double-layer segregations, GB splitting, and coupled shear-migration, depending on the details of interatomic interactions.