Nowadays, anodes based on graphitic materials are struggling with the ever-stringent requirements on lithium ion batteries (LIBs) in terms of energy and power densities, life-span, and deformability, from their extended applications such as automobiles, power grids and wearable electronics. As one of the promising alternates, transition metal oxides (TMOs) hold great perspectives. Unlike the lithium insertion mechanism of graphite, the lithiation/delithiation of TMOs is through redox conversion, imparting higher capacity and better safety. Among the numerous TMOs that have been extensively studied for LIB anodes, manganese oxides (MnO x ) are particularly attractive due to their high natural abundance, environmental benignity, tunable oxidation states, and low fabrication costs. However, as common to most of the TMOs, MnO x are essentially non-conductive and suffer from severe volume expansion upon lithiation, which greatly limit their rate capability and cycle performance. To overcome the above problems of MnO x (as well as other TMOs), many solutions have been attempted and can be majorly classified into two strategies: nanostructuring and carbon-compositing. The former based on developing diverse nanostructures brings in numerous benefits such as shortened ion diffusion path, enlarged electrochemically active surface, promoted electrolyte infiltration, as well as relieved lattice stress. The later based on hybridizing with various kinds of carbonaceous materials enables to greatly enhance electronic conductivity, buffer the cyclic volume fluctuation, and reinforce the electrode stability by providing structural supports for the active materials. Of the explored nanostructures, the yolk-shell structure has gained increasing attentions due to the prominent advantages in buffering the volume expansion and promoting the utilization of active materials. On one hand, when compared to solid nanoparticles the void spaces in the yolk-shell structure can accommodate the cyclic volume change during charge/discharge, effectively preventing the pulverization of active materials. On the other hand, in comparison to the hollow nanospheres and nanocages, the volumetric specific capacity of the yolk-shell structure is obviously superior. Nevertheless, despite of these apparent benefits, previous reported fabrications of yolk-shell nanostructures have been quite complex and typically involved multi-step synthesis with both high material and energy inputs. Besides, the structural stability and integrity of the yolk-shell structure itself pose an issue, in which the nanostructures might crack and collapse due to mechanical stress, especially in the prolonged charge/discharge process. Therefore, a rational design and facile fabrication of yolk-shell nanostructures for optimizing their utilization and stability in LIB anodes are highly desired for achieving the outstanding electrochemical and cycle performance. In this paper, a simple method involving polypyrrole-coated metal organic framework is adopted to synthesize manganese oxides with yolk-shell structure and use them as the anodes for lithium ion batteries. The as-prepared yolk-shell MnO x nanoparticles exhibit good specific capacity during charge/discharge, and demonstrate high specific capacities of 723, 651, 384 mAh g–1 at current densities of 0.1, 0.5 and 2 A g–1, respectively. Great stability and rate performance are also achieved with minimal capacity attenuation for over 200 cycles. Both the fabrication methodology and electrochemical understandings gained here for nanostructured manganese oxides can also extend to the other TMOs towards their ultimate implementation in high-performance LIBs.