Hierarchically structured microspheres consisting of carbon coated porous silicon have been prepared by a spray drying assisted magnesiothermic reduction using gelatin as carbon precursor and SiO2 as silicon source. Gelatin is deposited on the surface of SiO2 nanospheres during spray drying, which plays also as binder in assembling SiO2 nanospheres to form the microspheres. After the magnesiothermic reduction, gelatin is carbonized and deposited in-situ on the surface of nanospheres and porous silicon nanospheres wrapped with a carbon layer are derived. The thickness of carbon coating and the porosity of obtained Si/C composite nanospheres can be modified by tuning the content of gelatin in the suspension. Two desired purposes, i.e. downsizing of Si particles and in-situ carbon coating of the nanoparticles have been achieved by this preparation. The resulted Si/C composite microspheres show superior electrochemical performance and high structure stability as anode materials for Li-ion batteries. An initial reversible capacity of 1638 mAh g−1 and excellent capacity retention of 523 mAh g−1 after 300 cycles can be achieved at a current density of 200 mA g−1. The formation mechanism of the hierarchically structured microspheres and the variation of porosity for the individual Si nanospheres have been investigated and discussed in details.