Three-dimensional electron diffraction (3DED) has evolved into a mainstream method for nanocrystal structure determination, with widespread applications in structural biology, pharmaceutical research, functional materials, and Earth and planetary sciences. Here we report GIGED-1pro (Guangzhou Institute of Geochemistry Electron Diffractometer, first generation, professional version), a self-developed dedicated instrument for rapid nanocrystal structure determination. The instrument comprises a 120 kV Schottky thermal field emission gun as the electron source, a vertical column geometry, a 4-axis goniometer stage (drift < 200 nm over a ±50° tilt range), and a Dectris Quadro hybrid pixel direct electron detector. It integrates TEM imaging, continuous rotation electron diffraction (cRED) acquisition, and an automated data processing pipeline. Single-crystal structure determination of natural fluorapatite and calcite confirms that the instrument is capable of de novo structure solution of submicrometer mineral crystals. Batch phase screening was validated using Chang’e-6 lunar regolith as a complex unknown system. Unsupervised hierarchical clustering of 43 valid diffraction datasets successfully identified six mineral phases: cristobalite, clinopyroxene, olivine, andesine–labradorite, anorthite, and ilmenite. No priori phase assumption was required, and only trace powder was dispersed on a TEM grid. These results demonstrate that GIGED-1pro, through its dedicated and integrated design, achieves full-workflow coverage from nanocrystal structure determination to unbiased batch phase screening for mineralogical samples, demonstrating potential as an effective tool for low-consumption structural characterization of precious extraterrestrial returned samples and deep-Earth nanominerals. Its core design as a general-purpose nanocrystal electron diffraction platform may potentially be applicable to structural biology, pharmaceutical development, and functional materials research, though experimental validation in these additional fields remains for future work.