Pore-scale multiphase flow has always been a research hotspot petroleum engineering. However, the complexity of pore structure and the variability of the flow process have plagued researchers. More specifically, the controlling mechanisms behind mineral characteristics on brine flow behavior in shale at a pore-scale perspective are not well understood. So far, a limited number of scholars have tried to provide evidence of the underlying mechanisms based on integrated imaging and compositional methods, and the shale classification methods were mainly based on the content variation. This paper provided a new aspect concerning the mineralogical stratifications to investigate the controlling factors of movable fluid properties. Imaging and compositional techniques were used, and the samples with different mineralogical stratifications (inapparent grading sequence shale, apparent grading sequence shale, and microscopic block-shaped shale) were tested. Integrated methods showed that, compared to minerals compositions, the mineralogical stratifications would be more vital for storage capacity and fluid flow behavior in shales. Thick organic minerals bands or chunks would occlude the seepage paths, and pores below 100 nm might be the predominant storage spaces for shales. By combining the results of these methodologies, the pore size spectrum of shales can be determined more accurately. High movable fluid properties were observed for inapparent grading sequence shale. The mechanisms are discussed in terms of mineralogical stratifications and pore networks evolution Low porosity would decrease the movable fluid saturation due to the short storage spaces, and serious mineralogical stratification variations would restrict the flow path, leading to weak mobility of brine.