Partial crystallization in amorphous magnetic film is observed in this study. The film of Co46Fe46Zr5B3/Ru/Co46Fe46Zr5B3 (CFZB/Ru/CFZB) was prepared on glass substrate by DC magnetron sputtering. The CFZB underlayer (CFZB‐UL) and the CFZB overlayer (CFZB‐OL) were deposited under nominally same sputtering conditions, i.e. target, working gas, working pressure, input power, and deposition duration. The transmission electron microscopy (TEM) images with fast Fourier transform (FFT) patterns revealed that the CFZB‐UL was amorphous while the CFZB‐OL became unexpectedly partially crystallized. The result of X‐ray diffraction (XRD) spectra verified the TEM observation. The cause of the partial crystallization is attributed to the lower concentration of glass formers and the lattice matching between the overlayer and the Ru layer below.