We reported compositional separation(CS) into Co-enriched and Cri-enriched components inside the grains of Co-Cr based thin films prepared by rf sputtering. CS strongly depends on the sputtering conditions of substrate temperature and target composition. Tuning the microstructure of the Co-Cr films is important in order to employ the CS for high-density magnetic recording. We investigated the origin of CS from thermodynamic viewpoint. We employ a spinodal decomposition-like model to describe the origin of the CS in Co-Cr films. We consider the total free energy of the Co-Cr films as the sum of several free energies of; 1) thermodynamic mixing entropy of a binary solid solution, 2) magnetic ordering interaction(MOI) energy below the Curie temperature, and 3) excess interaction energy(XS) caused by the sputtering process as a function of temperature and composition. Those energies distorted the total free energy like the spinodal decomposition and caused the compositionally separated fine microstructure inside the grains. If the second derivative of the total free energy with respect to Cr composition becomes negative at a given substrate temperature, we may observe a metastable compositional separation inside the Co-Cr alloy films. We expect to exploit the microstructure of CS for ultra-high density magnetic recording.