Utilization of a novel two-dimensional coordination polymer generated from a trinuclear building block [Cu3(HSser)3(H2O)2]·2H2O (1) as a precursor in the synthesis of copper sulfide serendipitously resulted in CuS nanospheres with hollow interiors. The formation of CuS nanocrystals with the three-dimensional hierarchical flower-like morphology from the hydrogen-bonded metal complex [Cu(H2Sser)2]·H2O (2) as a precursor may be understood from the spatial arrangement of the metal atom and the organic ligand in the crystal lattice plays a major role in determining the shape of the nanomaterials. Detailed investigation on the effect of experimental conditions and the packing patterns of the complexes in the crystal lattice reveals the formation mechanism of the morphologically different CuS. The electrochemical behavior of these nanosized CuS meso-assemblies as a cathode material for lithium ion batteries reveals that the reaction proceeds through an insertion and deinsertion mechanism and the CuS with a hollow interior is more efficient and has good cyclability compared to that with a flower-like morphology.