Three-dimensional (3D) hierarchical nanostructures have generated a large amount of interest because of their unique, unusual properties and potential applications. In this article, copper(II) ions as the inorganic component and various biosurfactants as the organic component were used to successfully form 3D nanoflowers via a facile and effective self-assembly template synthesis strategy. It can be confirmed that the biosurfactant molecules can first form complexes with the copper ions, and these complexes then become nucleation sites for primary crystals of copper phosphate, indicating that the interaction between biosurfactant and copper ions leads to the formation of 3D nanoflowers. Several reaction parameters such as aging time and the concentration of the biosurfactant, which play a critical role in the formation process and morphologies of the nanoflowers, were investigated. Under the optimum synthetic conditions, a spherical flowerlike structure with hundreds of nanopetals was obtained. Moreover, the biosurfactant–Cu₃(PO₄)₂·3H₂O nanoflowers also showed high stability and catalytic activity for degradation of cationic dyes. Our results demonstrate that the biosurfactant–inorganic 3D nanoflowers, which combined the advantages of the biosurfactant and inorganic material, have potential applications in industrial biocatalysis, biosensors, and environmental chemistry.