The degradation at the glass fiber/matrix interface through molecular dynamics simulations in hygrothermal environment is investigated. The glass fiber reinforced polymer composite has been modeled using a cross-linked epoxy matrix and amorphous silica substrate. The degradation mechanism in hygrothermal environment is indicated through the reduction of decreased adhesion energy and the weakened intermolecular interactions with the consideration of hydration bond. Furthermore, softened epoxy molecules in hygrothermal conditioning possess a lower density near the fiber surface, which inhabits the stress transfer between fiber and matrix, eventually leading to the deteriorated interfacial adhesion. Our simulation results echo with the experimental measurements, which can be further calibrated and utilized as inputs in micromechanical models to bridge the gap between the macroscopic and microscopic behavior of civil infrastructures.