Silane coupling agents (SCAs) can improve fiber-resin interface issues, yet selecting an appropriate SCA experimentally is resource-intensive. Herein, a multi-level screening method combining simulation and experiments is proposed to identify SCA-enhancing bonding between SCAs and polyamide 66 (PA66) and the basalt fiber (BF) −PA66 interface. SCAs with organic groups composed of N and O exhibited superior interaction with PA66 due to the more pronounced negative and positive electrostatic potential (ESP) distributions. In SCAs-grafted BF-PA66 models, SCAs not only altered BF surface nanostructure but also changed the arrangement of PA66 main chains from parallel to interpenetrating BF surface atoms. Besides, (3-ureapropyl)trimethoxysilane (SCA6) significantly improved BF-PA66 bonding, which was experimentally validated by enhanced interlaminar shear and mechanical properties. O atoms on SCA6 and PA66 are more electronically bound and have the smallest ESP extremum, providing strong polar interaction sites. Additionally, both simulations and experiments demonstrated a transformation from adhesive to cohesive failure.