Self-assembly of vertically aligned nanocomposite films via spinodal decomposition is of potential interest in a range of technique applications. How the elastic interaction mediated by modulus mismatch, cubic anisotropy factor, and anisotropic lattice mismatch between the product phases facilitates the experimentally observed columnar nanocomposite formation was elucidated using three-dimensional phase field simulations of spinodal decomposition in an elastically inhomogeneous cubic binary epilayer. A phase diagram from vertically aligned columnar nanocomposites to vertically aligned laminar nanocomposites was constructed with respect to modulus mismatch, cubic anisotropy factor, and anisotropic lattice mismatch. The results provide a guideline for such nanocomposite structure formation.