Calcification exists in atherosclerotic plaques in the form of nanomineral aggregates and is closely related to the development of atherosclerosis. Spheroidal and massive calcification are two major types of calcification found in atherosclerotic tissue. However, the exact difference between these two types of calcification is still not clear. Samples composed entirely of spheroidal calcifications and massive calcifications were isolated from aortic atherosclerotic plaques and tested using both bulk and microscopic analysis techniques. Scanning electron microscopy and transmission electron microscopy showed that spheroidal calcifications had a core-shell structure. Massive calcifications were composed of randomly arranged nanocrystals. Synchrotron radiation X-ray diffraction, Raman spectroscopy and selected area electron diffraction showed amorphous calcium phosphate, whitlockite and carbonate hydroxyapatite all existing in spheroidal calcification, while massive calcification only consisted of carbonate hydroxyapatite. We conclude that amorphous calcium phosphate may act as a precursor phase of spheroidal calcifications that eventually transforms into a crystalline phase, while whitlockite in lesions could aggravate the progression of atherosclerosis.