A laser desorption postionization (LDPI) nanoscale resolution mass spectrometry imaging (MSI) technique based on a microlensed fiber is proposed for 3D imaging of microspheres which have a core-shell structure. Results show that the diameter of the sampling crater can be as small as 350 nm by introducing the desorption laser to the sample surface through the microlensed fiber. The use of laser postionization greatly solves the problem of weak signal caused by the very small sampling amount. A line scan of a sharp edge of Cr mesh shows that the imaging resolution of this method can reach to 300 nm. Through the imaging analysis of the alloy core-shell microspheres of Cr, Fe, Co, and Cu, the distribution of four elements at different positions can be observed visually. Particularly, the reconstruction 3D image of a single Nb-Zr core-shell particle demonstrates the potential of this technique in 3D imaging.