Spinodal decomposition in a binary thin film is studied by a three-dimensional (3D) phase field model. A cubic thin film with an (001) orientation is considered. The focus is on the effect of the types of substrate constraint on the morphological evolution during spinodal decomposition as compared to the corresponding bulk. The elastic strain effect is incorporated by solving the elasticity equations for an elastically inhomogeneous thin film with a free surface and constrained by a substrate. Temporal evolution for the composition field, and thus the morphological evolution, is obtained by solving the Cahn-Hilliard equation using a semi-implicit Fourier-spectral method. It is shown that a biaxial substrate constraint has essentially no effect on the spinodally decomposed two-phase morphology which is primarily controlled by the cubically anisotropic elastic interactions. The asymmetry in the strain components along the [100] and [010] directions from the substrate constraint results in the preferential alignment along one of the two directions. In the particular case of a harder phase whose lattice parameter increases with composition, a tensile substrate constraint along the film plane leads to the alignment of two-phase microstructures parallel to the tensile direction.