Magnetic circular dichroism (MCD) measures the differential absorption of a sample between the left and the right circularly polarized (LCP and RCP) light in the presence of a magnetic field, which is oriented in parallel with the direction of light propagation. MCD can be used to determine the absorptive difference between spin channels to resolve the polarized valence states in magnetic materials and/or provide new opportunity in understanding and modulation of excitonic and plasmonic resonances. In addition, polymer materials, as well as anisotropic crystalline with a specific internal electric field, will have a natural CD effect which can also be affected by a magnetic field. Nowadays, integrated polymer and magnetic materials have attracted increasing research attention in the area of organic spintronics and the interaction between magnetism and molecular chirality. One fundamental question that still remains is: can the MCD and natural CD effects be separated during MCD measurements using a simple method? In this work, we have constructed a rotational test fixture for rotational MCD measurements. We show the result of MCD measurement on the cobalt (Co) film/polymer and confirm that the proposed rotational MCD method is efficient for the separation of MCD and natural CD effects. We believe the results presented herein can open prospects for a distinct approach to study the magnetic material/polymer hybrid systems.