The three-dimensional (3D) structure of chromatin is important for gene regulation and transcription. It is very challenging to visualize different genomic loci in 3D space at large scale. Traditional Fluorescence in situ hybridization (FISH) can only label and visualize several (with the help of multi-color FISH) or very limited genomic loci or chromosomes (with the help of combination of different colors), because of the overlapping emission fluorescence signals. However, upconversion nanocrystals (UCNPs) convert infrared radiation to visible luminescence, thus are promising for bringing another dimension to visualize genomic loci in three-dimensional space. With the help of low-power super-resolution stimulated emission depletion (STED) microscopy, one can obtain sub-30nm resolution in images of the highly-doped UCNPs. Here we at first try to develop a novel method to label and visualize different genomic loci with UCNPs in fixed cell nuclei, then combine this method with traditional FISH, to visualize multiple genomic loci in genome. This strategy offers the new possibility to image 3D genome with high-throughput imaging.