As for organic flame retardants, the high dosages (up to 20 wt%) are usually required to achieve favorable flame retardancy, which often causes serious aggregation in epoxy resin (EP). Thus, the applications of flame retarded EP composites are restricted by the jeopardized mechanical property. Therefore, a nano-microarchitecture of MoS2 nanoflowers in-situ grown on polypyrrole microtube (P-Mo) is rationally constructed as flame retardant for EP. The peak heat release rate and total heat release are significantly reduced by 47.4% and 22.2%, when adding 3.0 wt% P-Mo, demonstrating the hindered heat release. Besides, the peak smoke production rate and peak CO yield show reductions of 46.8% and 62.9% separately, which proves the hindered toxicants emission. Thermogravimetric analysis/infrared spectrometry results also show the attenuated releases of toxic CO and NO. These results jointly demonstrate that using P-Mo can efficiently suppress the fire hazard of EP, ascribed to the physical barrier, chemical catalyzing and charring promotion actions. Surprisingly, the storage modulus value is enhanced by 20.9%, when only using 1.0 wt% P-Mo.