Embedding and tissue clearing with high refractive index reagents are essential for 3D tissue imaging. However, the current liquid-based clearing condition and dye environment suffer from solvent evaporation and photo-bleaching, causing difficulties in maintain the tissue optical and fluorescent features. In traditional embedding technique, paraffin is highly astigmatic and paraffin-tissue complex is opaque; CLARITY series of gel-type tissue transparency methods usually achieve cross-linking of tissue and gel network first, and then active or passive degreasing by using SDS, TritonX-100 and so on, and finally, the tissue achieves a transparent state by refractive index matching. Based on high permeability of deep eutectic solvents (DES) and the optical transparency potential of polyols, this study developed a DES self-assembled hydrogel-based copolymer to embed mouse tissue for clearing and imaging prepared with imidazole and d-sorbitol. In addition to preserving the high optic transparency of the tissue, the DES hydrogel system is compatible with multiple fluorescence labeling, particularly lipophilic dyes. This DES hydrogel system provides a unique opportunity for simultaneous tissue embedding and clearing. The self-assembled hydrogel achieves 3D imaging at a solid state, and 2D images can be obtained through slicing after 3D imaging of complete organs. Due to its temperature dependent hydrogel properties, the hydrogel-tissue complex achieves gel-sol transition and allows tissue reuse. This transparent and hydrogel condition provides a friendly tissue and cellular environment to facilitate high resolution 3D imaging, preservation, transfer, and sharing among laboratories to investigate the morphologies of interest in experimental and clinical conditions.