A 3D hierarchical flower‐like MgO microsphere was successfully obtained by pyrolysis of the flower‐like Mg5(CO3)4(OH)2·4H2O microsphere precursor which was itself synthesised by means of a facile and environmentally friendly hydrothermal route from MgCl2·6H2O. The possible formation process of the microsphere precursor was systematically investigated and considered to result from the following steps: (i) forming the 1D pillar‐like MgCO3; (ii) cracking to a 2D flake structure; (iii) assembling to the 3D flower‐like Mg5(CO3)4(OH)2·4H2O microsphere. The obtained close‐packed 3D flower‐like MgO microsphere has cubic symmetry and high crystallinity assembled by nanoflake particles with a mean diameter of 10 μm. Moreover, the heterogeneous catalysis of the Claisen–Schmidt condensation reaction between benzaldehyde and acetophenone to synthesise chalcones was also studied. The 3D flower‐like MgO microsphere exhibited better catalytic performance than that of commercial MgO and this was attributed to the especially 3D hierarchical flower‐like structure and the large surface area.