Hierarchical MoS2 microboxes constructed by ultrathin nanosheets are synthesized by a facile template-assisted strategy. The first step involves the L-cysteine assisted uniform growth of hierarchical MoS2 nanosheets on MnCO3 microcube templates which are at the same time converted to MnS. Hierarchical MoS2 microboxes can be obtained by selectively dissolving MnS through acid washing. When evaluated as an anode material for lithium-ion batteries, the hierarchical MoS2 microboxes manifest high specific capacity and excellent cycling performance. The hierarchical MoS2 microboxes also show enhanced electrocatalytic activity for electrochemical hydrogen evolution from water.