The relative atomic fraction of Cu(In,Ga)Se2 (CIGS) films is one of the most important measurements for the fabrication of CIGS thin film solar cells. However, the quantitative analysis of multi-element alloy films is difficult by surface analysis methods due to the severe matrix effect. In this study, the quantitative analysis of CIGS films was investigated by secondary ion mass spectrometry (SIMS). The atomic fractions of Cu, In, Ga and Se in the CIGS films were measured by alloy reference relative sensitivity factors derived from the certified atomic fractions of a reference CIGS film. The total ion intensities of the constituent elements were obtained by a total number counting method. The atomic fractions measured by SIMS were linearly proportional to those certified by inductively coupled plasma mass spectrometry using an isotope dilution method. The uncertainties were determined from the standard uncertainties in the measurements and those of a CIGS thin film certified reference material.