Tourmaline nanoparticles were prepared by using a wet mechanochemisty method. The X-ray diffraction (XRD) and scanning electron microscopy (SEM) results showed that the tourmaline grain size is in the range from tens of nanometers to several hundred nanometers. Through characterization by Fourier transform infrared spectroscope, it was found that the milled tourmaline had a better far infrared emitting performance due to the increase of radiation surface area. The structure change of liquid water clusters induced by the addition of tourmaline nanoparticles was observed by nuclear magnetic resonance (NMR). The results showed that the addition of tourmaline nanoparticles reduced the 17O NMR full width at half maximum intensity (FWHM) for treated water and the volume of water molecule clusters. The feature of activated water was enhanced with decreasing tourmaline nanoparticles size due to the cooperation of strong surface electric field and high far infrared emissivity. Moreover the activation time can be maintained at 480 h suggesting the potential application of tourmaline in wastewater treatment.