Shale formations exhibit multi-scale geological features such as nanopores in formation matrix and fractures at multiple length scales. Accurate prediction of relative permeability and capillary pressure are vital in numerical simulations of shale reservoirs. The multi-scale geological features of shale formations present great challenges for traditional experimental approach. Compared to nanopores in formation matrix, fractures, especially connected fractures, have much more significant impact on multiphase flows. Traditional flow models like Darcy's law are not valid for modeling fluid flow in fracture space nor in nanopores. In this work, we apply multiphase lattice Boltzmann simulation for unsteady-state waterflooding process in highly fractured samples to study the effects of fracture connectivity, wetting preference, and gravitional forces.