The invention discloses a precious metal core-shell structure nanoparticle which is of a double-layer structure, wherein a uniform shell-layer structure is formed by silicon dioxide nanoparticles with uniform granularity as a core which is continuously wrapped with silver nanoparticles; the nanoparticles are spherical granules; the particle size of the nanoparticles is not greater than 1[mu] m; the granularity of the nanoparticles is uniform. The invention further discloses a preparation and application of the nanoparticles in mass spectrometric detection. The precious metal core-shell structure nanoparticle is used in a matrix assistant laser analysis ionization spectrum and is capable of effectively eliminating background noise interference of a conventional organic matrix and improving an analysis ionization effect of a small-molecular substance. Small-molecular metabolin of an actual biological sample system can be effectively recognized and can be precisely quantified, the operation process is simple and convenient, and the detection efficiency can be greatly improved.