Graphene is possibly the thinnest membrane that could be used as a molecular separation gate. Several techniques including absorption, cryogenic distillation, adsorption, and membrane separation have been adopted for constructing separation systems. Molecular separation using graphene as the membrane has been studied because large area synthesis of graphene is possible by chemical vapor deposition. Control of the gate sizes is necessary to achieve high separation performances in graphene membranes. The separation of molecules and ions using graphene and graphene oxide layers could be achieved by the intrinsic defects and defect donation of graphene. However, the controllability of the graphene gates is still under debate because gate size control at the picometer level is inevitable for the fabrication of the thinnest graphene membranes. In this paper, the controlled gate size in the graphene sheets in single-walled carbon nanohorns (NHs) is studied and the molecular separation ability of the graphene sheets is assessed by molecular probing with CO2, O2, N2, CH4, and SF6. Graphene sheets in NHs with different sized gates of 310, 370, and >500 pm were prepared and assessed by molecular probing. The 310 pm-gates in the graphene sheets could separate the molecules tested, whereas weak separation properties were observed for 370 pm-gates. The amount of CO2 that penetrated the 310 pm-gates was more than 35 times larger than that of CH4. These results were supported by molecular dynamics simulations of the penetration of molecules through 300, 400, and 700 pm-gates in graphene sheets. Therefore, a gas separation membrane using a 340-pm-thick graphene sheet has high potential. These findings provide unambiguous evidence of the importance of graphene gates on the picometer level. Control of the gates is the primary challenge for high-performance separation membranes made of graphene.