Polymeric composites have attracted increasing interest in fundamental studies and industrial applications due to their often-superior characteristics over conventional pure polymers. In this work, we studied the relationship between the rheological properties, critical in processing methods such as additive manufacturing, and the structure of a polymer-2D filler system by experiment and simulation methods. Considering the high-performance polymer polyetherketoneketone (PEKK) with 2D filler (mica) composite as an example, the effects of filler size, filler content, surface chemistry and shear rate were systematically investigated. It is demonstrated that the interaction between the polymer and 2D filler brings two different consequences on tuning the viscosity of polymer-filler composite. The stronger interaction increases the shear stress of the polymer-2D filler composite system, leading to higher viscosity. On the other hand, the stronger interaction can promote more adsorption of polymer chains on the surface and form ordered structure in short range, which will make the local polymer network disentangled and decreases the continuous viscosity from the polymer network for entangled polymer system. This work provides a fundamental understanding on the relationship between macroscopic rheological properties and the structural properties and energetics at molecular level of polymer-2D filler composite.