With special tubular and skeletal bauplan, Ediacaran tubular fossils are one unique metazoan group that has irreplaceable significance for our understanding of the early metazoan evoution. However, their biological affinities have long been disputed because of their limited morphological features and ambiguous primary composition. In all the recorded taxa, this problem typically existed with Cloudina and Sinotubulites, the two most important tubular fossils which have stratigraphic and evolutionary significances. Here we carried out a detailed study on their microstructure, mineralogical composition and taphonomic background, for the purposes of revealing their taphonomic characteristics and biomineralogical potentials which may shed light on the understanding of their phylogenetic affinities. Phosphatic and calcitic specimens from the Yangtze Block, Namibia, and Paraguay were studied using integrative approaches including EBSD, Raman spectroscopy, and cathodoluminescence. It was revealed that, excluding the influence of diagenesis, crystal orientations in all studied Cloudina and Sinotubulites lack an ordered alignment which are commonly seen in biomineralization processes. In most specimens, the luminescence between the surrounded rocks and the fossils showed no diagenetic related differentiation, indicating no traces of original carbonatization. Besides, Raman spectroscopy analysis showed intense carbon within the parallel laminae of tube walls in contrast to the surrounding rocks among both phosphatic and carbonatic taphono-facies preserved which may be residue of original organic matters. These analyses altogether suggest that the original tube-wall composition of both Cloudina and Sinotubulites was likely organic with no detectable traces of primary biomineralization.