Synchrotron-based scanning transmission X-ray microscopy (STXM) efficiently integrates X-ray microscopy and X-ray absorption spectroscopy (XAS) to provide quantitative, chemically specific imaging of elements, functional groups, bonding, and oxidation states in 2D and 3D modes at high spatial resolution (sub-10 to 30 nm), high energy resolution, and low radiation doses. STXM has been increasingly used to study various materials and samples for life, earth, planetary, and environmental sciences. In this progress report and minireview, the STXM principle and instrumentation of conventional STXM and the latest STXM-ptychography at the Canadian Light Source are first discussed. Then, two representative applications of STXM on geoscience-related samples, including magnetotactic bacteria, soil microaggregates, and related systems, are presented to illustrate the strong capabilities and suitability of STXM to elucidate complex systems, processes, and associations in the natural sciences. Finally, the potential applications and prospects of the STXMrelated techniques in characterizing precious extraterrestrial samples (e.g., lunar samples returned by China's Chang'e-5 mission) are briefly discussed.