Morphology of the active layer in bulk heterojunction P3HT:PCBM organic solar cell was studied using Monte Carlo (MC) and coarse-grained dynamics simulations. While coarse-grained molecular dynamics allow us to quickly estimate the P3HT:PCBM interfacial energy of bilayer structure as a function of underlying layer thickness, bridging the dimension and time gap between dynamics simulations and experiment is computationally expensive and therefore not viable. Using MC technique with input from dynamics simulations allowed us to speed up the calculation and obtain final morphological information based on energetics and entropy, and at the same time retained the physics fidelity in-built in our validated coarse-grained model. The final structure gives phase separated domains with dimension of approximately 12 nm, on par with reported experimental result. The method can be applied to other organic photovoltaics systems to predict active layer morphology relevant for device performance or 3-dimensional device modelling at continuum level.