Abscisic acid (ABA) is an essential plant hormone responsible for plant development and stress responses. Recent structural and biochemical studies have identified the key components involved in ABA signaling cascade, including PYR/PYL/RCAR receptors, protein phosphatases PP2C, and protein kinases SnRK2. The plant-specific, Roh-like (ROPs) small GTPases are negative regulators of ABA signal transduction by interacting with PP2C, which can shut off “leaky” ABA signal transduction caused by constitutive activity of monomeric PYR/PYL/RCAR receptors. However, the structural basis for negative regulation of ABA signaling by ROP GTPases remain elusive. In this study, we have utilized large-scale coarse-grained (10.05 milliseconds) and all-atom molecular dynamics simulations and standard protein-protein binding free energy calculations to predict the complex structure of AtROP11 and phosphatase AtABI1. In addition, we have elucidated the detailed complex association pathway and identified the critical residue pairs in AtROP11 and AtABI1 for complex stability. Overall, this study has established a powerful framework of using large-scale molecular simulations to predict unknown protein complex structures and elucidated the molecular mechanism of  negative regulation of ABA signal transduction by small GTPases.