Embryo-like fossils from the early Ediacaran Weng'an biota provide a window of exceptional fossil preservation onto the period of life history in which molecular clocks estimate the fundamental animal lineages to have diverged. However, their diversity and biological affinities have proven controversial, because they are morphologically simple and, consequently, their interpretation lacks phylogenetic constraint. The subcellular structures preserved in these embryo-like fossils might help to understand their cytology, biology, and diversity, but the potential of these structures has not been fully realized, because detailed microscale physical and chemical investigations are lacking. Here, to remedy this deficiency, we performed a comprehensive study to characterize their micro- and ultra-structures as well as in-situ chemical components. Our results reveal three types of subcellular structure that differ in size, shape, and mineral components: (1) relatively small and spheroidal granules in embryo-like fossils with equal cell division pattern; (2) relatively large, spheroidal, or polygonal granules in embryo-like fossils with unequal and asynchronous cell division pattern; and (3) irregular multi-layered rim-bounded granules in embryo-like fossils with unequal and asynchronous cell division pattern. We propose that the three types may be rationalized to a single taphonomic pathway of preferential mineralization of the cell cytoplasm, preserving an external mould of subcellular granules. We followed the previous interpretation that the spheroidal and polygonal granules should be fossilized lipid droplets or yolk platelets. The distinction between these subcellular structures are largely the result of postmortem degradation processes such as autolysis. The widely preserved lipid droplets or yolk platelets within these Ediacaran embryo-like fossils are compatible with the interpretion of large yolky embryos with maternal nourishment and direct development.