Water-based drilling fluids find extensive application in drilling operations for the removal of drilling waste and the enhancement of drilling efficiency, owing to their remarkable thixotropic properties. Thixotropy in drilling fluids is intricately connected with the evolution of their internal structure. Most existing structural dynamics models that address thixotropy are tailored for waxy crude oils and oil-based suspensions, making it challenging to accurately characterize the rapid changes in the internal structure of water-based drilling fluids. In this study, we propose a novel structural dynamics model based on the constitutive models with both isotropic and kinematic hardening (IKH). This model elucidates the thixotropic properties and structural evolution characteristics of water-based drilling fluids by incorporating the rheological coefficient and the structural damage rate index. Through verification using constant shear rate and hysteresis loop experiments, the proposed model in this paper precisely describes the rheological behavior of water-based drilling fluids (including the phenomenon of stress overshoot), besides, faithfully depicts the distinctive thixotropic structural evolution of it.