Statistical fragments and micro-failure modes in the multi-fiber-reinforced micro-composites were investigated by fragmentation test. The specimen consisted of three fibers using carbon fibers (CFs) and glass fibers (GFs), embedded in the epoxy resin with three-dimensional arrangement. Fracture morphology and micro-failure behavior from the progressive fragmentation of fibers and fiber/matrix interfacial adhesion were observed via polarized-light microscope. The interfacial shear strength of CF/epoxy micro-composites is higher than that of the GF/epoxy micro-composites measured by the single fiber fragmentation test. The results show that fragment number on monofilament demonstrates obvious differences between multi-fiber and single fiber systems, and the location of the breakpoint is determined by the CFs that fracture firstly, indicating clustering fracture modes. This is because stress concentration around the breakpoints influences the stress redistribution on the adjacent fibers. Distinct micro-failure modes were observed in three-fiber and the hybrid systems, where matrix cracks around the CFs and interfacial debonding occurs around the GFs. The mixture of CFs and GFs demonstrates distinctive hybrid effect by the changes of the fragment number and initial fracture strain of fibers in hybrid systems.