In this work, highly flexible MoS2-based lithium-ion battery anodes composed of disordered thin MoS2 nanoflakes encapsulated in amorphous carbon nanofibrous mats were fabricated for the first time through hydrothermal synthesis of graphene-like MoS2, followed by electrospinning and carbonization. X-ray diffraction as well as scanning and transmission electron microscopic studies show that the as-synthesized MoS2 nanoflakes have a thickness of about 5 nm with an expanded interlayer spacing, and their structure and morphology are well-retained after the electrospinning and carbonization. At relatively low MoS2 contents, the nanoflakes are dispersed and well-embedded in the carbon nanofibers. Consequently, excellent electrochemical performance, including good cyclability and high rate capacity, was achieved with the hybrid nanofibrous mat at the MoS2 content of 47%, which may be attributed to the fine thickness and multilayered structure of the MoS2 sheets with an expanded interlayer spacing, the good charge conduction provided by the high-aspect-ratio carbon nanofibers, and the robustness of the nanofibrous mat.