Selectivity control is a challenging goal in Fischer–Tropsch (FT) synthesis. Hydrogenolysis is known to occur during FT synthesis, but its impact on product selectivity has been overlooked. Demonstrated herein is that effective control of hydrogenolysis by using mesoporous zeolite Y-supported cobalt nanoparticles can enhance the diesel fuel selectivity while keeping methane selectivity low. The sizes of the cobalt particles and mesopores are key factors which determine the selectivity both in FT synthesis and in hydrogenolysis of n-hexadecane, a model compound of heavier hydrocarbons. The diesel fuel selectivity in FT synthesis can reach 60 % with a CH4 selectivity of 5 % over a Na-type mesoporous Y-supported cobalt catalyst with medium mean particles sizes of 8.4 nm (Co) and 15 nm (mesopores). These findings offer a new strategy to tune the product selectivity and possible interpretations of the effect of cobalt particle size and the effect of support pore size in FT synthesis.