New possibilities offered by the method of secondary ion mass spectrometry (SIMS) for analysis of the phase composition of carbon-containing materials are considered. Differences are established between the mass spectra of three carbon phases: diamond, diamond-like carbon (DLC), and graphite. A simple algorithm for the quantitative determination of different phases in two-phase systems diamond–graphite and DLC–graphite is proposed that is based on the measurement of relative intensities of secondary cluster ions such as C_8/C_5 and CsC_8/CsC_4. It is shown that nonuniform depth profiles of various carbon phases are formed in diamond structures upon laser cutting and in DLC structures upon thermal annealing.