Self-assembled three-dimensional Ni−Al layered double hydroxide (LDH) nanostructures have been successfully synthesized using a facile biopolymer-assisted approach in the presence of a simple, safe, and inexpensive sodium alginate biopolymer under hydrothermal conditions. The structure and morphology of LDH nanostructures obtained have been investigated by scanning electron microscopy (SEM), powder X-ray diffraction (XRD), high-resolution transmission electron microscopy (HRTEM), Fourier transform infrared spectroscopy (FT-IR), thermogravimetric and differential thermal analysis (TG-DTA), and UV−visible diffuse spectroscopy (UV−vis). Three types of pompon-like, marigold-like, and coral-like LDH nanostructures could be obtained by adjusting the synthesis parameters including hydrothermal aging time, concentration of metal ions, and reaction temperature. A possible formation mechanism for the controlled organization of primary LDH nanosheet building units into special three-dimensional nanostructures is proposed on the basis of the interaction between sodium alginate molecules and LDH crystals. Furthermore, after calcination of LDHs at 500 and 700 °C, the resulting NiO-based mixed metal oxides still maintain the three-dimensional morphology of their LDH precursors to some extent, indicative of the high thermal stability of nanostructures. The findings in this work provide a feasible approach for the morphosynthesis of LDH nanomaterials with special superstructures.