Organic and inorganic materials are usually added to polymers in order to achieve some benefits such as reducing the product cost, as well as achieving higher modulus and strength. Addition of these materials would change polymers’ behavior. Adding nano-materials to polymers on the other hand is a new challenge in the field of polymer composites where previous studies were unable to achieve good correlation with nano-composites at higher particle volume fractions. In this research, Yamamoto network theory is developed to investigate the behavior of highly nano-filled systems. For this purpose, five different types of sub-chain and two types of junctions are considered and the effect of particle size, concentration, and the model parameters in association with the behavior of the junctions are studied. Moreover, some experiments are performed on polystyrene filled with nano-silica at different particle size and concentration values in frequency mod in the linear region. At last, we compared the results of our final model with the experiments in order to evaluate its accuracy, which confirmed a very good agreement. © 2016, © The Author(s) 2016.