In shale reservoirs, spontaneous imbibition is an important mechanism of fracturing fluid loss, which has an important impact on enhanced oil recovery and water resource demand. However, spontaneous imbibition behaviors are more complicated to characterize and clarify due to the nanoscale effects of the boundary slip, oil-water interfacial slip, and heterogeneous fluid properties caused by intermolecular interactions. A nanoscale multi-relaxation-time multicomponent and multiphase lattice Boltzmann method was applied to investigate the water imbibition into oil-saturated nanoscale space. The effects of pore size, fluid-surface slip, water film, oil-water interfacial slip, water bridge, and pore structures on the imbibition behaviors in a single nanopore were investigated. Then, the spontaneous imbibition behaviors in nanoporous media based on the pore scale microsimulation parameters obtained from the molecular simulation velocity results were simulated, and the effects of water saturations on imbibition behaviors were discussed. The results show that as the water saturation increases from 0 to 0.1, the imbibition mass in nanoporous media increases because of the oil-water interfacial slip and a completely hydrophilic wall. As water saturation continues to increase, the imbibition mass decreases gradually because the existence of water bridges impedes the water imbibition.