X‐ray computed tomography (CT) has become a critical technique in the study of porous media. It has attracted growing attention for analyzing hydrate‐bearing sediment, but this has been done using surrogates (Xe/Kr) only due to difficulties in distinguishing methane hydrate from water. This study presents the successful imaging of methane hydrate coexisting with pore liquid, gas, and sediments. We used potassium iodide (KI) solutions and in‐line propagation‐based phase‐contrast CT analysis of X‐ray attenuation and diffraction to distinguish the four materials. Thus, consideration for CT‐related X‐ray physics was necessary to optimize KI concentrations, improve material separation with X‐ray propagation, and properly interpret artifacts within the images. The images clearly show methane hydrate in the pore space of sand (~250 μm) coexisting with KI solution and gas. Following this, X‐ray CT can now be used to visualize pore habits of natural methane hydrate in sediment cores. Plain Language Summary Methane hydrate has great potential as an energy resource. Thus, the behavior of methane hydrate in reservoirs is the current focus of research for gas production and environmental impacts. It is critical to know how hydrate is distributed in sediment pores and how it interacts with sediments in order to understand the potentially dynamic physical and chemical properties of hydrate‐bearing sediments. This study develops an X‐ray computed tomography technique to gain 3‐D insight into sediment pores with resolution down to micron level, while maintaining high pressure and low temperature during the scan to keep methane hydrate stable. This technique takes advantages of both the attenuation and interference of X‐ray waves. Attenuation characteristics of materials of interest are manipulated with enhancing agents to achieve optimum contrasts. X‐ray wave interference is utilized to enhance edge detection between different materials. Our results establish the ability of the proposed techniques to discern methane hydrate from its hosting environment. The proper interpretation of results relies on the fundamental understanding of X‐ray physics so that artifacts induced by X‐ray wave interference can be discerned from real features of interest on material surfaces. The technique can be utilized for various aspects of geomaterial characterization. Key Points Methane‐hydrate coexisting with pore liquid, gas, and sediment are 3‐D visualized at pore scale Image contrasts among different materials are enhanced via optimizing X‐ray attenuation and diffraction Brighter‐darker pair pattern resulted from X‐ray diffraction could lead to erroneous interpretation