As the size of magnetic devices continuously decreases, the creation of three-dimensional nanomagnets and the understanding of their magnetic configurations become increasingly important for modern applications. Here, by progressive nucleation during epitaxial nanoelectrodeposition, we synthesize single-crystal iron nanocuboids with sizes ranging 10 to 200 nm on one sample. The size-dependent magnetic configurations of these nanocuboids are studied by quantitative magnetic force microscopy and electron holography. In conjunction, a "magnetic configuration versus size" phase diagram is established via micromagnetic simulations. Both experiment and theory reveal a sequential transition from Landau pattern to vortex and finally single domain when decreasing the sizes of the nanocuboids. The combinatorial-like approach leads to a quantitative understanding of the magnetic configurations of the nanomagnets in a broad size range. It can be transferred to other materials and shapes and thereby presents an advanced route to enrich the material library for future nanodevice design.