Coal seam water injection technology could improve the water content of coal seam, which is an effective technical measure to reduce dust generation in the mining process. Water-based silica nanofluids are a green wetting agent for coal seam water injection. To understand the wetting mode of nanofluids in coal, it is necessary to explore the physico-chemical properties of nanofluid-modified coals. First, a new idea of saturation and intrusion of nanofluid into coal was proposed by using vacuum pressurized saturation device. Then, the physical and chemical properties of the modified coal were studied by Fourier transform infrared spectrometer, low-temperature liquid nitrogen adsorption experiments, and uniaxial compression mechanics experiments. The results showed that the content of oxygen-containing functional groups in the modified coal increased, which was positively correlated with the concentration of nanofluids. The pore structure of the modified coal sample changed from complex to simple, and the nanoparticles blocked the micropores to make the coal surface smooth. The saturation invasion of SiO2 nanofluids changed the mechanical properties of coal samples, and the compressive resistance of coal was weakened, and the minimum strength of the coal invaded by 1.5 wt. % SiO2 nanofluid saturation was 13.68 MPa. The saturation intrusion of SiO2 nanofluids has a negative effect on the surface adsorption of coal samples and the blockage of microporous structures, and makes the coal seam easier to be wetted, which contributes to the application and development of nanofluids in the field of coal seam water injection.