Domain configuration in epitaxial antiferroelectric films has been studied by X-ray nanoscopy, with the extraction of information about the domain sizes beyond the beam-size limit. The objective of this article is to understand how film thickness (the cases of 50 and 1000 nm are explored) and temperature (20 and 200°C) affect the nanodomain configuration of PbZrO3/SrRuO3/SrTiO3 thin films. It is found that the majority of antiferroelectric domains in both films are too small to be directly mappable, because many of them are simultaneously illuminated by the nanobeam (60 × 100 nm) most of the time. Nevertheless, these small sizes can be studied by analysing the diffraction peak width, which is, in the simplest approximation, inversely proportional to the domain size. With this approach it is identified that the characteristic (most probable) domain size does not depend on the film thickness and is ∼13 nm, while the scarcer larger domains do depend on it. An increase of the temperature to 200°C (just below the nominal antiferroelectric-to-cubic transition temperature) results in a slight increase in the characteristic size. These results are compared with those in ferroelectric films, where domain sizes are pronouncedly thickness dependent, and the relevant methodological question on the possibility of neglecting the interference of X-ray waves scattered by different nanodomains in the nanodomain assembly is also discussed.