Removing unwanted materials, such as organic coatings and soil, from the cultural relic surface is a complex and significant task in the field of cultural heritage conservation. Microemulsion-loaded gel can effectively and safely remove those organic coatings and soil. Here, we employed a simple solvent exchange strategy to prepare a microemulsion-loaded polyvinyl alcohol/polyethyleneimine (PVA/PEI) hydrogel. First, PVA and PEI were dissolved into DMSO to form a gel. Then, the gel was immersed into a microemulsion composed of water, ethyl acetate, propylene carbonate, sodium dodecyl sulfate, and 1-pentanol to exchange DMSO. Microemulsion-loaded PVA/PEI hydrogel can be synthesized by completely substituting DMSO. To investigate the microstructure, rheological properties, and mechanical properties of the gel, scanning electron microscopy, a rheometer, and a universal testing machine were used, respectively. Fourier transform infrared (FT-IR) analysis was conducted to explore the synthesis mechanism and confirm the successful loading of microemulsion within the microemulsion-loaded PVA/PEI hydrogel. Furthermore, FT-IR, a depth-of-field microscope, and a glossmeter were utilized to evaluate the cleaning efficiency of the microemulsion-loaded PVA/PEI hydrogel for removing animal glue and soil from the surfaces of cultural relics. Moreover, an X-ray fluorescence spectrometer was used to analyze the element component of the ancient coin. The application results showed that the microemulsion-loaded PVA/PEI hydrogel can effectively remove animal glue from an ancient wall painting surface. Moreover, it is capable of removing soil from an ancient coin surface as well, which helped to confirm the age of the coin. This offers a novel method to prepare microemulsion-loaded hydrogel and demonstrates great potential in the cleaning for cultural heritage.