Microdigitate stromatolites (MDS), a kind of important sedimentary structures in the Neoarchean to Mesoproterozoic carbonates, have long been explained as the products of sea floor precipitates and are of abiogenic origin, for their prominent fibrous fabrics in interior but without recognizable microbial fossils. In this study microscope, FESEM and EDS were used to characterize the microfabrics at micron to nanometer scales in the Mesoproterozoic silicified MDS from the North China Platform. The study shows that the MDS microscopically consist of alternating light and dark laminae of sub millimeter scale. The light micro sparitic laminae, about 65μm in average thickness, contain fewer of bacterial relics, and have suffered obvious recrystallization during early diagenesis; whereas the dark micritic laminae are rich in bacterial relics, sub oval clumps or micropeloids of 10~50μm in diameter, which are often encased variably by micro sparitic rims of 2~10μm wide. The dark micritic laminae include two types: the D1 laminae (about 380μm thick) are characterized by having vertically denser and transversely continuous sub laminae (about 15μm thick), and the D2 laminae (about 300μm thick) are developed with sparser and discontinuous sub laminae. Hairy suberect fibers can be observed throughout the MDS columns, but less clear in the light laminae than in the dark ones. The fibers may have resulted either from mineralized bacterial filament bundles with suberect growth pattern or from concentrated micropeloids that are aligned vertically to the laminae. The micropeloids are made up of numerous polyhedrons interwoven with bacteria filaments and EPS with which abundant nanoparticles (<45nm in size usually) are closely associated. The nanoparticles tend to coalescence into submicron scaled polyhedrons that may have functioned as seeds for subsequent crystal growth (i.e., carbonate nucleation), and the polyhedrons in turn, with bacterial filament relics, further aggregate into micropeloids. The micro sparitic rims encasing the micropeloids and the micro sparitic strips at sides of the fibers contain rarely bacterial relics, and are likely formed through microbially influenced precipitation, while the micritic fibers and micropeloids are likely from microbially induced precipitation. Thus, the widespread MDS in the Mesoproterozoic carbonates of North China should be biogenic origin. Furthermore, the organomineralization mechanism revealed in the MDS may shed light to the genetic explanation of even older stromatolites, and the ordered assembly of organominerals from nanoparticles to micropeloids in the MDS may also exist in other microbialites, which may potentially be used as biosignatures for the recognition of biogenic carbonates.