Dissipative particle dynamics Simulations were performed oil phosphonic acid-functionalized copolymer melt. This copolymer consists of poly (ether-ether-ketone) and poly(p-vinylhenylphosphonic acid) blocks. Three different mapping schemes were implemented to obtain the morphology in different length scales. The morphology obtained from the simulation of the copolymer when mapped in correspondence to experimentally obtained polymer showed a similar morphology to that obtained from scanning tunneling and atomic force microscopy. The simulations show that the poly (ether-ether-ketone) blocks aggregate in small Clusters embedded by poly(p-vinylbenzylphosphonic acid) blocks. Two further mapping schemes were undertaken to elucidate the phase behavior in p-vinylbenzylphosphonic acid blocks in Molecular scale. The results obtained from the simulations, as, well as the new identified morphologies provide useful information for synthesizing a new set of polymers which could be important to show promise for fuel cell application.