Two-dimensional MoS2 is a promising anode material for Li-ion batteries, but suffers from poor electrochemical activity and stability. Herein, a facile approach for the controlled synthesis of onion-like nanospheres organized by carbon encapsulated MoS2 nanosheets is developed through a simple polymerization and sulfidation/carbonation process. Mo-containing polyoxometalate is demonstrated to enable polymerization of polypyrrole accompanying with uniform encapsulation of Mo-nanoclusters. The hybrid precursor confines the growth of few layer MoS2 nanosheets (<= 5 layers) into N-doped carbon framework, which is of great benefit in enhancing the electrical conductivity and structural integrity. As a result, the nanospherical MoS2@C hybrid electrode manifests high Li-ion storage capacity (1119 mAh g(-1) at 0.1 A g(-1)), excellent rate capability (616 mAh g(-1) at 2 A g(-1)), and long cycling stability. The substantial improvement is rationalized by fast electrode kinetics and great pseudocapacitive contribution. The present work may offer a powerful engineering strategy of MoS2@C nanomaterials for Li/Na-ion batteries and electrocatalysts.