Understanding the optimal processing conditions for the fabrication of polymer nanocomposites is of fundamental importance in designing materials with balance of properties. To understand these conditions in the case of maleic anhydride grafted polypropylene (PP-g-MA)/layered mesostructured silica (LMS) nanocomposites, the effect of temperature, shear rate, and residence time during processing on the structure of the nanocomposites were studied. The results showed that the combination of temperature, residence time, and mechanical shears have strong effect on the structure of the nanocomposites, rather than just interfacial interactions between the polymer matrix and silicate layers. However, interfacial interactions between the polymer matrix and silicate layers primarily play an important role to the intercalation of polymer chains into the silicate galleries. On the basis of our experimental results, a first explanation of the formulation mechanism of PP-g-MA/LMS nanocomposites is proposed. Finally, a general concept of processing conditions for manufacturing of polymer nanocomposites by melt-compounding process in a batch-mixer is described.