In this work we use a three-dimensional Pauli master equation to investigate the charge carrier mobility of a two-phase system, which can mimic donor-acceptor and amorphous-crystalline bulk heterojunctions. Our approach can be separated into two parts: the morphology generation and the charge transport modeling in the generated blend. The morphology part is based on a Monte Carlo simulation of binary mixtures (donor/acceptor). The second part is carried out by numerically solving the steady-state Pauli master equation. By taking the energetic disorder of each phase, their energy offset and domain morphology into consideration, we show that the carrier mobility can have a significant different behavior when compared to a one-phase system. When the energy offset is non-zero, we show that the mobility electric field dependence switches from negative to positive at a threshold field proportional to the energy offset. Additionally, the influence of morphology, through the domain size and the interfacial roughness parameters, on the transport was also investigated.