Atom probe tomography (APT) can quantitatively analyze three-dimensional elemental and isotopic distributions of different elements in a solid sample at sub-nanometer resolution. It has been increasingly used in geochemical analysis. In this work, using two planetary minerals and one silicate glass standard as examples, we study the practicability and accuracy of the APT method in the quantification of chemical composition. Comparison of the results obtained using electron probe microanalysis (EPMA) and APT show that the APT results are close to those from EPMA with the difference of major metal element contents is less than 1 at%, while the difference of silicate glass is much larger. In addition, the difference of oxygen content in all samples is about 1-3 at% due to the limitations of the APT method. However, this oxygen difference can be corrected by normalization using metal elements. Our analyses suggest that APT can be an effective method to quantify major elements in materials. The threedimensional distributions of elements given by APT can be used to the element migration process at nanoscale, which is a new and important technique for geochemical analysis.