Carbon materials with particular morphologies, structures and sizes are highly desired for different application purposes which can be normally derived from transition metals- and rare earths-based metal organic frameworks (MOFs). However, little is known about MOFs synthesized using main group metals. Herein, we derived a three-dimensional (3D) pomegranate-like structure of porous carbon microspheres (PCMSs) formed by self-assembly of hollow highly-graphitized thin-walled nanoballs by directly carbonizing indium-MOFs (CPM-5). The formation of this unique 3D porous hierarchical structure is closely related to the presence of indium with a low melting point and its effect of catalyzing carbon graphitization, which is demonstrated to be a robust sulfur host for high performance lithium-sulfur (Li–S) batteries. The S/PCMSs electrodes with the areal sulfur loadings of 2.0 and 4.3 mg cm−2 deliver the capacities of 1239 mAh g−1 (742 mAh g−1) at 0.2 C (4 C), and 941 mAh g−1 (480 mAh g−1) at 0.2 C (4 C), respectively, with the low capacity decay rates of 0.014%/cycle over 500 cycles at 4 C, and 0.060%/cycle over 900 cycles at 2C, respectively. The superior performance is attributed to the effective physical confinement of polysulfides as a result of highly dispersed sulfur nanoclusters separated by thin carbon walls, the superior conduction arising from the porous highly graphitized conductive networks and the stable 3D structure due to the compact self-assembly of hollow nanoballs compared to dispersed hollow carbon microspheres or nanoparticles. The unique 3D Pomegranate-like structure as a new morphology and structure enriches the carbon material family which is expected to have other potential applications such as electrode materials for lithium ion batteries, catalysis and chemical adsorption.