The development of multi-shelled hollow carbonate nanospheres (MHCN) for biomedical applications is challenging, and has not been reported. In this study, a facile approach is firstly reported to synthesize hierarchically porous MHCN with controllable shell numbers using a novel strategy called layer-by-layer thermal decomposition of organic acid salts and templates. The choice of organic acid salts as the reactants is innovative and crucial. The shell numbers of porous MHCN can be easily controlled and tuned through adjusting the adsorption temperature of organic acid salts and/or the adsorption ability of the template. The synthetic method can not only open a window to prepare the multi-shelled carbonates but also provide a new strategy to synthesise other multi-shelled inorganic salts. Notably, the hierarchically porous multi-shelled hollow structures empower the carbonates with not only a large specific surface area but also good porosity and permeability, showing great potential for future applications. Herein, our in vitro/vivo evaluations show that CaCO3 MHCN possess a high drug loading capacity and a sustained-release drug profile. It is highly expected that this novel synthetic strategy for MHCN and novel MHCN platform have the potential for biomedical applications in the near future.