C2H4O2 isomers, methyl formate (HCOOCH3), acetic acid (CH3COOH) and glycoaldehyde (HOCH2CHO), have been detected in a lot of sources in ISM. However, their abundances are very different, with methyl formate much more abundant than the other two isomers. This fact may be related to the different destruction by ionizing radiation of these molecules. The goal of this work is experimentally study the photodissociation processes of methyl formate and acetic acid ices when exposed to broadband soft X-ray from 6 up to 2000 eV. The experiments were performed coupled to the SGM beamline in the Brazilian Synchrotron Light Source (LNLS/CNPEM) at Campinas, Brazil. The simulated astrophysical ices (12K) were monitored throughout the experiment using infrared vibrational spectroscopy. The analysis of processed ices allowed the determination of the effective destruction cross sections of the parent molecules as well as the effective formation cross section of daughter molecular species. The relative abundance between acetic acid and methyl formate (NCH3COOH/NHCOOCH3) in different astronomical scenarios and their column density evolution in the presence of X-rays were calculated and our results suggests that such radiation field can be one of the factors that explain the difference in the isomers C2H4O2 abundances. We also quantified the daugther species after the establishment of a chemical equilibrium in the samples.