We present the results obtained from a study of the variability of iron emission lines in the high mass X-ray binary pulsar Cen X-3 during the eclipse, eclipse-egress and out-of-eclipse phases using XMM-Newton observations. Three iron emission lines at 6.4 keV, 6.7 keV, and 6.97 keV are clearly detected in the spectrum of the pulsar during the entire observations, irrespective of different binary phases. The properties of these emission lines are investigated at different intensity levels. The flux level and equivalent width of the emission lines change during the eclipse, eclipse-egress and out-of-eclipse orbital phases. Based on the results obtained from the time resolved spectral analysis, it is understood that the most probable emitting region of 6.4 keV fluorescent line is very close to the neutron star whereas the other two lines are produced in a region that is far from the neutron star, probably in the highly photo-ionized wind of the companion star or in the accretion disk corona.