Samples of ZnO and ZnO:Mn nanocrystals with Mn 2 and 4 at.% impurity concentrations obtained by ultrasonic spray pyrolysis were studied by X-ray diffraction. It was determined that the reflexes of the X-ray diffractions of the samples had a shift relative to the standard position towards large diffraction angles. This indicated the nonequilibrium state of the crystal lattice, which caused the appearance of strain stresses. Debye–Scherrer and Williamson–Hall methods were used to calculate the parameters of the crystal lattice, the size of nanocrystals, and strain stresses with different concentrations of Mn. When the concentration of Mn increased to 4 at.%, there was an increase in strain stresses in nanocrystals by 10 times in comparison with undoped ZnO. The unit cell volume of ZnO:Mn nanocrystals was significantly smaller in comparison with single-crystal ZnO, which indicated that they had their intrinsic defects.