The hygroscopicity of Y2Mo3O12 has serious influences on its mechanic and negative thermal expansion (NTE) properties. The reported partial ion substitution for Y3+ in Y2Mo3O12 could reduce the hygroscopicity, however, the expected NTE properties disappear disappointedly. In this investigation, it is found that avoiding the invasion of crystal water and extending the NTE temperature range of Y2Mo3O12 to room temperature could be realized together by heating with CO(NH2)2. The X-ray diffraction patterns, infrared absorption spectra, scanning electron microscopy images and X-ray photoelectron spectra suggest the formation of small hydrophobic molecules (C3N4, C, etc.) coated on the surface, which could clog the microchannels in Y2Mo3O12 to avoid the invasion of crystal water. The investigation paves a way to improve the NTE properties by neglecting the influences of water molecules on the stretching vibrations of MoO4 tetrahedra and the transverse vibrations of bridge oxygen atoms.