New samples returned by China Chang’e-5 (CE-5) mission offer an opportunity for studying the lunar geologic longevity, space weathering, and regolith evolution. The age determination of the CE-5 samples was among the first scientific questions to be answered. However, the precious samples, most in the micrometer size range, challenge many traditional analyses on large single crystals of zircon developed for massive bulk samples. Here, we developed a non-destructive rapid screening of individual zirconium-containing particle for isotope geochronology based on a Micro X-ray fluorescence analysis (µXRF). The selected particles were verified via scanning electron microscopy (SEM), 3D X-ray microscopy (XRM), and focused ion beam scanning electron microscopy (FIB-SEM) techniques, which showed that zirconium-bearing minerals with several microns were precisely positioned and readily suitable for site-specific isotopic dating by second ion mass spectrometry (SIMS). Such protocol could be also applicable in non-destructively screening other types of particles for different scientific purposes. We therefore proposed a correlative workflow for comprehensively studying the CE-5 lunar samples from single particles on nanometer to atomic scales. Linking various microscopic and spectromicroscopic instruments together, this workflow consists of six steps: (1) single-particle selection with non-destructive µXRF technique, (2) 2D/3D morphological and structural characterization with a correlative submicron 3D XRM and nanoscale resolution FIB-SEM imaging methods, (3) SEM analysis of the surface morphology and chemistry of the selected particle, (4) a series of microscopic and microbeam analyses (e.g., SEM, electron probe microanalysis, and SIMS) on the cross-section of the selected particle to obtain structural, mineralogical, chemical, and isotopic features from the micron to nanometer scale, (5) advanced 2D/3D characterization and site-specific sample preparation of thin foil/tip specimens on a microregion of interest in the selected particle with FIB-SEM technique, and (6) comprehensive analyses on the FIB-milled specimens at nanometer to atomic scale with synchrotron-based scanning transmission X-ray microscopy, analytic transmission electron microscopy, and atom probe tomography. Following this technical roadmap, one can integrate multiple modalities into a uniform frame of multimodal and multiscale correlated datasets to acquire high-throughput information on the limited or precious terrestrial and extraterrestrial samples.