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The study addresses the effect of thermal treatment on the internal structure of polyelectrolyte multilayers (PEMs). In order to get insight into the internal structure of PEMs, Neutron Reflectometry (NR) was used. PEMs with a deuterated inner block towards the substrate and a non-deuterated outer block were prepared and measured in 1% RH and in D2O before and after a thermal treatment. Complementarily, PEMs with the same number of layers but completely non-deuterated were investigated by ellipsometry. The analysis for the overall thickness (d), the average scattering length density (SLD) and the refractive index (n) indicate a degradation of the PEM. The loss in material is independent of the number of layers, i.e., only a constant part of the PEM is affected by degradation. The analysis of the internal structure revealed a more complex influence of thermal treatment on PEM structure. Only the outermost part of the PEM degenerates, while the inner part becomes denser during the thermal treatment. In addition, the swelling behavior of PEMs is influenced by the thermal treatment. The untreated PEM shows a well pronounced odd—even effect, i.e., PDADMAC-terminated PEMs take up more water than PSS-terminated PEMs. After the thermal treatment, the odd-even effect becomes much weaker.