The elemental composition and microscopic-level shape of inclusions inside industrial materials are considered important factors in fracture analytical studies. In this work, a three-dimensional (3D) microscopic elemental analysis system based on a serial sectioning technique was developed to observe the internal structure of such materials. This 3D elemental mapping system included an X-ray fluorescence analyzer and a high-precision milling machine. Control signals for the X-ray observation process were automatically sent from a data I/O system synchronized with the precision positioning on the milling machine. Composite specimens were used to confirm the resolution and the accuracy of 3D models generated from this system. Each of the two specimens was composed of three metal wires of 0.5 mm diameter braided into a single twisted wire that was placed inside a metal pipe; the pipe was then filled with either epoxy resin or Sn. The milling machine was used to create a mirror-finish cross-sectional surface on these specimens, and elemental analyses were performed. The twisted wire structure was clearly observed in the resulting 3D models. This system enables automated investigation of the 3D internal structure of materials as well as the identification of their elemental components.