High-energy thermal treatments, such as electron beam irradiation, are crucial for enhancing the performance of tungsten carbide–cobalt (WC-Co) composites in cutting tools and wear-resistant coatings. This study utilizes molecular dynamics simulations to analyze the nanoscale effects of such treatments on WC-Co surfaces, focusing on cobalt evaporation and linear scratching phenomena. The results demonstrate that electron beam irradiation significantly accelerates cobalt evaporation, with rates depending on energy flux and local atomic environments. Embedded cobalt atoms within WC grains exhibit higher resistance to evaporation due to stronger bonding, while pure cobalt surfaces show greater susceptibility to material loss. Under high energy flux, WC-Co surfaces experience an interplay of thermal expansion, density reduction, and evaporation, resulting in accelerated degradation. Linear scratching simulations reveal that thermally treated WC-Co surfaces exhibit increased structural instability, as indicated by broader distributions of local entropy and von Mises stress, reflecting heightened susceptibility to deformation and failure. Stress concentrations from indentation and scratching are more pronounced in thermally treated samples, highlighting the influence of thermal history on mechanical behavior. Molecular dynamics simulations enable detailed insights into atomic-scale phenomena, allowing precise quantification of the effects of energy flux, material composition, and thermal treatment on structural and mechanical responses. These findings emphasize the need to optimize thermal treatment protocols to enhance the durability and performance of WC-Co composites, providing valuable guidance for the development of robust materials for industrial applications.