Despite tremendous interest in graphene due to its superior electrical and remarkably strong mechanical properties, its semi-metallic property (zero bandgap) causing extremely low on/off-current ratio has still prevented integrating successfully graphene-based electronic applications. Although several approaches were reported to overcome this weak point, such as graphene nanoribbon, graphene nanoconstriction, graphene quantum dot, and dual-gated bilayer graphene, sufficiently high on/off-current ratio for logic applications was not demonstrated yet. Recently, in order to resolve the low on/off-current ratio, vertical graphene-based heterojunction barristors were proposed, where the drain current in the barristor devices is controlled by adjusting the barrier height between graphene and another semiconductor through gate biasing. These barristors were based on heterojunction with another class of atomically thin two-dimensional (2D) materials named transition metal dichalcogenides (TMDs) including molybdenum disulfide (MoS2), molybdenum diselenide (MoSe2), tin disulfide (SnS2) and tungsten disulfide (WS2), tungsten diselenide (WSe2).[1-4] Because the TMD materials have high scalability, excellent junction interface quality, and low contact resistance, the vertical graphene/TMD heterojunction barristors are expected to be used for future low-power wearable devices. However, the graphene layer on SiO2 that was normally used as a gate dielectric in the above works suffers from a charge puddle effect. Specifically, because the charge puddle phenomenon seems to degrade the performance of the graphene barristors by limiting modulation of the Fermi level of graphene, it is very important to suppress the charge puddles on graphene. In addition, most researches related with graphene/TMD heterojunction barristors remained on the level of qualitative analysis of device operations, consequently hindering further optimization and development. Here, we theoretically and experimentally investigated the influence of the graphene Fermi level position on the performance of a graphene/TMD heterojunction barristor. Then, we optimized the graphene/TMD heterojunction devices fabricated on MoS2 and WSe2 by suppressing charge puddle effect. Through a 3-aminopropyltriethoxysilane (APTES) treatment, which was applied in order to block the charge puddles on graphene, the on/off-current ratio values were improved by a factor of 32 and 230 in the graphene/MoS2 and graphene/WSe2 heterojunction barristors, respectively. Finally, based on first-principle density functional theory (DFT) calculations coupled with temperature-dependent current-voltage measurements and a theoretical analysis model, we quantitatively studied the atomistic origins of the operation mechanism in the graphene/TMD heterojunction barristors. [1] Y.-F. Lin, W. Li, S.-L. Li, Y. Xu, A. Aparecido-Ferreira, K. Komatsu, H. Sun, S. Nakaharai, K. Tsukagoshi, Nanoscale 2014, 6, 795-799. [2] W. J. Yu, Z. Li, H. Zhou, Y. Chen, Y. Wang, Y. Huang, X. Duan, Nat. Mater. 2013, 12, 246-252. [3] Y. Sata, R. Moriya, T. Yamaguchi, Y. Inoue, S. Morikawa, N. Yabuki, S. Masubuchi, T. Machida, J. J. Appl. Phys. 2015, 54, 04DJ04. [4] T. Georgiou, R. Jalil, B. D. Belle, L. Britnell, R. V. Gorbachev, S. V. Morozov, Y.-J. Kim, A. Gholinia, S. J. Haigh, O. Makarovsky, L. Eaves, L. A. Ponomarenko, A. K. Geim, K. S. Novoselov, A. Mishchenko, Nat. Nanotechnol. 2013, 8, 100-103.