Rubber-based conductive polymer composites are deformable and flexible, which have been demonstrated tremendous applications in electromagnetic interference (EMI) shielding materials. Here, we filled different dimensional carbonaceous fillers, including zero-dimensional carbon black (0D CB), one-dimensional carbon nanotubes (1D CNTs), two-dimensional graphene (2D GP), and their combinations, into isoprene rubber (IR) to fabricate the flexible EMI shielding composites. Both the electrical, mechanical, and EMI shielding properties were investigated. It was found that the EMI shielding properties of IR-based composites mainly dominated by the microwave absorption consumption. Since 1D CNTs possess the highest EMI shielding effectiveness for absorption, IR/CNTs composites exhibit the best electromagnetic interference shielding properties compared to other carbonaceous nanoparticles filled composites. Moreover, partially replacing CNTs with CB particles to fabricate hybrid IR/CB/CNTs composite is an effective route to improve the electrical properties and lower the cost of the composites. However, it is found that hybrid IR/CB/CNTs composite has a lower EMI shielding effectiveness than IR/CNTs composites, indicating that EMI shielding properties depend on a lot more than just the electrical conductivity of the resulting composites. Nevertheless, based on comprehensive consideration of cost, electrical, mechanical and EMI shielding properties of the composites, it is still an effective way to design the high-performance EMI shielding materials via the combination of different dimensional fillers.