Water-oil displacement is an important process that occurs in a shale matrix after hydraulic fracturing and in water-based enhanced oil recovery. Current understanding of this displacement process is limited because of the complicated pore structure and surface properties in shale. In this work, this process and its controlling factors are investigated through a comparative study of three shale samples that have different types of pore systems and wettability. An integrated method of imbibition and multiscale imaging was applied, and a modified oleic tracer that can better represent oil flow was used in imbibition testing and micro-computed tomography (CT) imaging. Scanning electron microscope (SEM) pore characterization was then performed under high magnification with guidance from the micro-CT images showing the changes caused by oil or water imbibition. New insights were obtained on the importance of both wettability and pore size effect on oil recovery and the distribution of residual oil after water-oil displacement. Connectivity of pores with different wettability is also discussed based on 3D analysis and SEM pore characterization. Collectively, these new findings improve the understanding of the complicated process of water-oil displacement and the role of influencing factors. Important implications for improved oil recovery strategy in shale are discussed for different types of reservoir rocks. The integrated imaging and imbibition technique provides a new path for further investigation of improved oil recovery in shale.