Corneal nano-nipple structures consisting of hexagonally arranged protrusions with diameters around 200 nm have long been known for their antireflection capability and have served as biological blueprint for solar cell, optical lens and other surface designs. However, little is known about the global arrangement of these nipples on the ommatidial surface and their growth during the eye development. This study provides new insights based on the analysis of nano-nipple arrangements on the mesoscale across entire ommatidia, which has never been done before. The most important feature in the nipple structures are topological 5- and 7-fold coordination defects, which align to form dislocations and interconnected networks of grain boundaries that divide the ommatidia into crystalline domains in different orientations. Furthermore, the domain size distribution might be log-normal, and the domains demonstrate no preference in crystal orientation. Both observations suggest that the nipple growth process may be similar to the nucleation and growth mechanisms during the formation of other crystal structures. Our results are also consistent with the most recently proposed Turing-type reaction-diffusion process. In fact, we were able to produce the key structural characteristics of the nipple arrangements using Turing analysis from the nucleation to the final structure development.