We have developed a new ion source using massive molecules called a metal cluster complex. The use of ion beams of metal cluster complexes allows for a layer-by-layer sputtering technique, resulting in accurate measurement of trace amounts of elements in samples. The ion source is compact enough to be installed in commonly-used secondary ion mass spectrometry (SIMS) systems. With the ion source, we have performed SIMS analysis of boron-doped silicon samples, thereby demonstrating that high depth resolution of less than 1nm can be obtained at a beam energy of 5 keV. In addition to inorganic materials, it also allows one to analyze organic materials with higher sensitivity and lower damage. Hence, we expect that the ion source will have great potential in SIMS analysis of various materials such as heterogeneous and biomedical materials.