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Polypyrrole (PPy) is the most studied material among the conducting polymers for high‐performance supercapacitors. However, due to morphology collapse, polypyrrole exhibits poor cycling ability and lower charge storage capacity, limiting its real‐world applications. To address these issues herein, the binary nanocomposites of PPy with MoS2 (molybdenum disulfide) NSs (nanostructures) in two different morphologies, that is, cenosphere (PPyC) and nanotubes (PPyNTs), have been prepared through in situ polymerization technique. The electrochemical performances of PPyC/MoS2 and PPyNTs/MoS2 nanocomposite are compared to define the most favorable morphology when PPy nanostructures are utilized as the electrode materials for creating flexible supercapacitors. The rational design of PPyNTs/MoS2 nanocomposite consisting of dense wrapping of PPyNTs on MoS2 leads to high specific capacitance (Csp) up to 481 F/g at 0.5 A/g. After 2000 charge‐discharge cycles, a decline of 5.6% in the specific capacitance of PPyNTs/MoS2 nanocomposite was observed, primarily attributed to the presence of chemically active sites on MoS2 nanosheets. This led to a strong alignment with the nitrogen group of pyrrole rings in the polymer chain to form a robust interconnected framework between tubular PPy and sheet‐like MoS2. This outstanding performance of PPyNTs/MoS2 nanocomposite resulted in designing futuristic flexible supercapacitors. [ABSTRACT FROM AUTHOR]