While substantial advances were made in pore system characterization in shale in the past decade, understanding of fundamentals of multiphase fluid flow in shale remains limited. The complexity of multiphase fluid flow in shale is related to many factors including nanoscale to submicron‐scale pore systems, differences in mineralogy and associated surface wettability, heterogeneity of these properties at different scales, and possible existence of microfractures. Previous work related to fluid flow, such as permeability measurement, spontaneous imbibition, and wettability analysis, includes many simplified assumptions/hypotheses with limited consideration of small‐scale details. In addition, these studies were mostly focused on single‐phase phenomena. Direct observation of multiphase fluid flow in shale showing small‐scale details is highly desired. In this study, dynamic imaging using synchrotron‐based micro‐CT (computed microtomography) was conducted on two shale samples to investigate multiphase (oil and water) spontaneous imbibition. The results revealed many details of multiphase flow in shale, including pore connectivity, porosity and permeability layered distribution, and wettability of microfractures and pores. At the same time, results illustrate the complexity of multiphase flow in shale and gaps in understanding that need further investigation.