A major obstacle of the selective inhibitor design for specific human phosphodiesterase (PDE) is that highly conserved catalytic pockets are difficult to be distinguished by inhibitor molecules. To overcome this, a feasible path is to understand the molecular determinants underlying the selectivity of current inhibitors. BAY60-7550 (BAY for short; IC₅₀ = 4.7 nM) is a highly selective inhibitor targeting PDE2A which is a dual-specificity PDE and an attractive target for therapeutic intervention of the central nervous system (CNS) disorders. Recent studies suggest that molecular determinants may be in binding processes of BAY. However, a detailed understanding of these processes are still lacking. To explore these processes, High-Throughput Molecular Dynamics (HTMD) simulations were performed to reproduce the spontaneous association of BAY with catalytic pockets of 4 PDE isoforms; Ligand Gaussian Accelerated Molecular Dynamics (LiGaMD) simulations were performed to reproduce the unbinding-rebinding process of FKG and MC2, two pyrazolopyrimidinone PDE2A selective inhibitors, in the PDE2A system. The produced molecular trajectories were analyzed by the Markov state model (MSM) and the molecular mechanics/generalized Born surface area (MM/GBSA). The results showed that the non-covalent interactions between the non-conserved residues and BAY, especially the hydrogen bonds, determined the unique binding pathways of BAY on the surface of PDE2A. These pathways were different from those of BAY on the surface of the other three PDE isoforms and the binding pathways of the other two PDE2A inhibitors in PDE2A systems. These differences were ultimately reflected in the high selectivity of this inhibitor for PDE2A. As a result, this study demonstrates the critical role of the binding processes in the selectivity of BAY, and also identifies the key non-conserved residues affecting the binding processes of BAY. Thus, this study provides a new perspective and data support for the further development of BAY-derived inhibitors targeting PDE2A