Formation of ordered structure in flux-grown Ba(Mg1/3Ta2/3)O3(BMT) single crystals was studied using x-ray diffraction, electron diffraction, and high-resolution electron microscopy. The low-temperature-grown crystals exhibited no sign of B-site ordering. Annealing at 1500 °C induced the 1:2 ordered phase, and its content increased with the annealing time. The superlattice diffraction peaks were broad initially; they sharpened rapidly with the annealing time. Diffuse superlattice reflections were found in electron diffraction patterns of 1500 °C annealed BMT; they turned into sharp reflections under long annealing time or higher temperature, 1600 °C. The intensity of diffuse reflections was sparsely distributed, but the maximum intensity location was determined in the digitized recording of image plate. The maximum intensity sites of two diffuse reflections in the 〈111〉 direction deviated from the presumed 1/3 and 2/3 positions and shifted towards the center. The diffuse reflection and the deviation from regular positions were interpreted as the composition modulation during B-site cation diffusion.