Advances in thermal sprayed coatings have been exciting in past decades. There is no doubt that the performances of the coatings are dependent on their microstructure and clarification of the microstructure on the other hand gives rise to better understanding on their properties. The characterization of the splats itself is significantly decided by the progress of characterization techniques. The knowledge of the microstructures inside individual splats is yet lacking so far. Focused ion beam (FIB) system uses a Ga ⁺ ion beam to raster over the surface of a sample in a similar way as the electron beam in a scanning electron microscope. The generated secondary electrons (or ions) are collected to form an image of the surface of the sample. The ion beam allows the milling of small holes with a big variety of shapes in the sample at well localized sites, so that cross-sectional images of the structure can be obtained or that modifications in the structures can be made. In this study, the internal nanostructural features of thermal sprayed hydroxyapatite (HA) splats were disclosed and characterized using the FIB. The FIB provides the advantages that the splat was removed layer by layer with controlled layer thickness (several nanometers to 1mm) and the microstructure was recorded by a electron microscopy affiliated to the FIB. The first layer HA splat was found to be composed with columnar nanosized grains and the other layer splats were recognized to be with spherical nanosized grains. Further interesting nanostructural features and nanosized pores were recognized inside the splats and their formation mechanism was also discussed.