At present, a single technical method has difficulty in obtaining microscopic data of ultra-light elements, trace elements, and crystal structures in samples simultaneously. This work combined an in situ focused ion beam—transmission electron microscopy—time of flight secondary ion mass spectrometry (FTT) technique and analyzed the composition and crystal structure of four phyllosilicate samples. These materials were comprised of antigorite, clinochlore, and cookeite phases. An FIB sample preparation technique was found to provide a sample thickness suitable for TEM observations and a degree of surface roughness appropriate for TOF-SIMS analysis. In addition, the relative amounts and distributions of various elements could be obtained, as well as crystal structure data, such that the composition and crystal structure of each specimen were determined. The in situ FTT method demonstrated herein successfully combines the advantages of all three analytical techniques and offers unique advantages with regard to analyzing ultra-light and trace elements as well as the structural data of phyllosilicates.