Analysis and characterization of micro/nano-sized pore structure are critical issues in shale geology and engineering. Scanning electron microscopy (SEM) imaging is one of the most widespread methods for the analysis of the micro/nano-sized pores in shale, but precise identification of the ultrafine pore structure in shale is still a big challenge because shale is so complex that some components may have overlap with pores based on the simple discrimination of gray scale under SEM microscopy. Here, Fe3O4/Au nanocomposite with magnetic properties is synthesized, characterized, and introduced as a novel pore-marker to improve SEM identification and quantitation of micro/nano-sized pores in shale. Due to the superparamagnetic property, the nanomarker is conveniently controlled by an external magnetic field to fill into pores and offers a sharp contrast imaging between matrix of shale (various gray) and pores (bright), which makes the identification of micro/nano-sized pores in shale much more straightforward and reliable. Furthermore, because gold, as a noble metal, is particularly rare in shale, energy-dispersive X-ray spectroscopy mapping of Au is delicately used to precisely calculate area porosity in shale. Combining with the aforementioned merits of the nanomarker, a precise and practical technique is proposed to promote characterization of micro/nano-sized pores in shale.