We present a microscopic description for generation of 1/f noise in interfaces between cobalt thin film and silicon substrate. Along with surface resistance measurements and transmission electron diffraction observations. 1/f noise power spectral density has been measured for the interfacial structures at the liquid nitrogen temperature . The cobalt films have been deposited by the electron-beam evaporation technique onto p-type (100) silicon in the high vacuum condition. The measured noise power spectral density shows highest magnitude near the structural transition and metallization transition region. The noise magnitude rapidly decreased after the cobalt silicide nucleation. The noise parameter is concluded to be originated form the structural fluctuations.