Nano-porous nano-silicon (npn-Si) anode for Li-ion battery is a great promise to mitigate problems associated with large volume expansion and pulverization during the charging-discharging cycle. Here we report the synthesis of highly porous Si from MCM-41, through a magnesiothermic reduction ((MR) method. Structural studies confirm the complete conversion of MCM-41 to crystalline silicon from the particle core to the surface. Morphological studies reveal the retention of porous network in the parent compound after reduction. The silicon anode is fabricated using two types of aqueous binders viz Na salt of carboxymethyl cellulose (Na-CMC), alginate (Na-Alg) demonstrates good cycling stability and rate performance. Among these, porous silicon with former binder shows a higher initial charge capacity of 2767 mAhg−1 even at a current rate of C/2 and retains 705 mAhg−1 capacity after 500 cycles. While, alginate binder showed much higher initial capacity of 3000 mAhg−1 and retained almost the same capacity as Na-CMC after 10 cycles and beyond. High capacity and reasonably good retention of nano-porous nano-silicon is attributed to (i) the accommodation of the drastic volume change in porous Si to effectively mitigate the mechanical stress, (ii) enhanced electrochemical kinetics and (iii) high Li flux in the porous structure.