Femtosecond laser ionization time-of-flight mass spectrometry (fs-LI-TOFMS) is introduced for the three-dimensional elemental analysis of a Nantan meteorite. Spatially resolved multielemental imaging of major and minor compositions in a meteorite are presented with a lateral resolution of 50 μm and a depth resolution of 7 μm. Distinct 3D distributions of siderophile, lithophile, and chalcophile elements are revealed. Co and Ni are highly siderophile (Iron-loving), mainly enriched in the metal phase. Cr, Cu, V, and Mn are enriched in the sulfide for their chalcophile (S-loving) tendency. S, P, and C aggregate together in the analytical volume. Silicate inclusion, containing lithophile elements of Al, Ca, Mg, K, and so on, is embedded within the metal phase for the immiscibility between silicate inclusion and the melted metal phase. These 3D distributions of elements aid the exploration of the formation and evolution of the meteorite. They also reveal the feasibility of fs-LI-TOFMS as a versatile tool for 3D imaging.