The rough contact plays an important role in the adhesion of carbon fiber/polymer matrix interface and interface modeling techniques are integral to quantify the effects of roughness factors on material properties. Taking the popular CF/PEEK materials as the object, an atomic method is proposed to construct CF/PEEK rough interfaces in this paper, which adopts a sinusoidal form to change the roughness regularly. Based on molecular dynamics (MD) simulations, CF/PEEK tensile separation experiment is processed and the response of the CF/PEEK interfaces with different roughness under mechanical loading are investigated. Based on the recorded CF/PEEK atomic force-displacement behavior, innovating roughness parameters, a traction separation law for the interface region is proposed. This study found the contact area between the two phases, which can be greatly improved through rough structures, determines the interfacial adhesion strength. In addition, this study observes interesting phenomena through the capturing atomic states, such as the polymer chains at the boundary between the two phases are greatly stretched.