In this study, we report about the occurrence of phase separation through spinodal decomposition (SD) in spinel manganese ferrite (Mn ferrite) thin films grown by Dynamic Aurora pulsed laser deposition. The driving force behind this SD in Mn ferrite films is considered to be an ion-impingement-enhanced diffusion that is induced by the application of magnetic field during film growth. The phase separation to Mn-rich and Fe-rich phases in Mn ferrite films is confirmed from the Bragg’s peak splitting and the appearance of the patterned checkerboard-like domain in the surface. In the cross-sectional microstructure analysis, the distribution of Mn and Fe-signals alternately changes along the lateral (x and y) directions, while it is almost homogeneous in the z-direction. The result suggests that columnar-type phase separation occurs by the up-hill diffusion only along the in-plane directions. The propagation of a quasi-sinusoidal compositional wave in the lateral directions is confirmed from spatially resolved chemical composition analysis, which strongly demonstrates the occurrence of phase separation via SD. It is also found that the composition of Mn-rich and Fe-rich phases in phase-separated Mn ferrite thin films deposited at higher growth temperature and in situ magnetic field does not depend on the corresponding average film composition.