Flexible energy-storage devices have attracted growing attention with the fast development of bendable electronic systems. However, it still remains a challenge to find reliable electrode materials with both high mechanical flexibility/toughness and excellent electron and lithium-ion conductivity. This paper reports the fabrication and characterization of highly porous, stretchable, and conductive polymer nanocomposites embedded with carbon nanotubes (CNTs) for application in flexible lithium-ion batteries. The systematic optimization of the porous morphology is performed by controllably inducing the phase separation of polymethylmethacrylate (PMMA) in polydimethylsiloxane (PDMS) and removing PMMA, in order to generate well-controlled pore networks. It is demonstrated that the porous CNT-embedded PDMS nanocomposites are capable of good electrochemical performance with mechanical flexibility, suggesting these nanocomposites could be outstanding anode candidates for use in flexible lithium-ion batteries. The optimization of the pore size and the volume fraction provides higher capacity by nearly seven-fold compared to a nonporous nanocomposite.