The laminated structure of continental shale oil reservoirs introduces significant macro and micro heterogeneity, posing challenges for efficient shale oil extraction. Existing microscopic experimental and simulation methods are insufficient to accurately simulate the fluid flow behavior in mud–lime interactive laminated shale reservoirs. This study delves into the complexities of laminated shale reservoirs with a focus on their heterogeneous structure and wettability. Using scanning electron microscopy, we extracted the structural features of laminated shale reservoirs and established a Multicomponent and multiphase -multi relaxation time-Lattice Boltzmann model(MCMP-MRT-LBM) that considers nanoscale effects such as wall adsorption, liquid–solid slippage, and liquid–liquid slippage. We investigated the occurrence state, the flow behavior, and the phase seepage characteristics of crude oil in laminated shale at different water saturation stages and explored the reasons behind interlayer channeling and the conditions under which crude oil is mobile within limestone and mudstone layers. Then, we examined the impact of varying factors, including heterogeneous wettability, displacement pressure gradients, and pore size, on relative permeability, water injection capacity, sweep efficiency, and crude oil recovery in laminated reservoirs. The results indicate that wettability and pore size distribution, driven by capillary and viscous forces, dictate the occurrence state of remaining oil. Wettability primarily influences fluid distribution, whereas pore size distribution substantially impacts fluid morphology. It also highlights the pivotal role of flow velocity differences between layers in causing interlayer channeling. Increasing the capillary number promotes crude oil mobility within mudstone layers, with the initiation pressure gradient in mudstone layers being 2.5 times that of the limestone layer. The examination of the oil–water relative permeability reveals the dominance of pressure gradients in affecting oil flow capabilities, while pore size significantly influences water flow capacity. By optimizing various factors, it is possible to enhance water injection capacity and sweep efficiency, resulting in a substantial 5%–10% increase in crude oil recovery from laminated shale reservoirs.