Transition metal oxides have attracted great attention as an anode material for next generation lithium ion batteries. Here we report the preparation of self-assembled hierarchical 3D-NiO microspheres with ultra-thin porous nanoflakes by simple and cost effective urea assisted chemical co-precipitation method followed by annealing at different temperature. It is noteworthy that the annealing temperature has an impact on the formation of different morphologies and resultantly on the electrochemical performance. This hierarchical 3D-NiO microspheres with ultra-thin porous nanoflakes shows enhanced electrochemical performance with a large reversible capacity, superior cyclic performance, high rate capability, and improved ionic conductivity as an anode material for lithium ion batteries. A high reversible capacity up to 795 mA h g−1 after 150 cycles at a rate of 0.5 C, and a capacity higher than 460.2 mA h g−1 at a rate as high as 10 C were obtained for optimized NiO sample. In particular, enhancement of the electrochemical performance was attributed to the high specific surface area, good electric contact among the particles, and easier lithium ion diffusion.