To meet the comprehensive demand for flexible microwave absorbing (MA) materials, a novel MA rubber containing homemade Polypyrrole nanotube (PPyNT) is produced based on the natural rubber (NR) and acrylonitrile-butadiene rubber (NBR) blends. To achieve the optimal MA performance in the X band, the PPyNT content and NR/NBR blend ratio are adjusted in detail. The 6 phr PPyNT filled NR/NBR (90/10) composite has the superior MA performance with the minimum reflection loss value of −56.67 dB and the corresponding effective bandwidth of 3.7 GHz at a thickness of 2.9 mm, which has the merits in virtue of achieving strong absorption and wide effective absorption band with low filler content and thickness compared to most reported microwave absorbing rubber materials over the same frequency. This work provides new insight into the development of flexible microwave-absorbing materials.