Flower‐like Cu3[MoO4]2O microspheres have been synthesized by using a sequential process from lindgrenite (Cu3(MoO4)2(OH)2). Lindgrenite nanoflowers were synthesized through a simpler route by using an aqueous chemical precipitation technique at room temperature without any surfactants or template. Subsequently, 3D flower‐like Cu3[MoO4]2O microspheres have been synthesized by annealing at 300 °C for 2 h from lindgrenite (Cu3(MoO4)2(OH)2). From the XRD pattern, FTIR spectrum, SEM and TEM analysis, flower‐like Cu3[MoO4]2O (ca. 5 μm) microspheres have been obtained, which were assembled from 3–4 nm thick nanosheets with an orthorhombic structure. Application of 3D flower‐like microspheres as an anode material for lithium‐ion batteries (LIBs) has been investigated and the possible electrochemical mechanism is analyzed. Electrochemical characterization of the Cu3[MoO4]2O nanoflowers as an anode material for LIBs has exhibited good cycle stability and a high coulombic efficiency during operation. The electrochemical activity was attributed to the unique structure of the Cu3[MoO4]2O microspheres, which provide more active sites for Li‐ion storage as well as a reduced transfer resistance. This work has explored a simple synthesis strategy for the synthesis of flower‐like Cu3[MoO4]2O microspheres without templates, additives, or surfactants, which exhibit a basis for not only high electrochemical performance in reversible Li storage, but also cycle stability.