The ability to control the stacking structure in layered materials could provide an exciting approach to tuning their optical and electronic properties. Because of the lower symmetry of each constituent monolayer, hexagonal boron nitride (h-BN) allows more structural variations in multiple layers than graphene; however, the structure-property relationships in this system remain largely unexplored. Here, we report a strong correlation between the interlayer stacking structures and optical and topological properties in chemically grown h-BN bilayers, measured mainly by using dark-field transmission electron microscopy (DF-TEM) and optical second harmonic generation (SHG) mapping. Our data show that there exist two distinct h-BN bilayer structures with different interlayer symmetries that give rise to a distinct difference in their SHG intensities. In particular, the SHG signal in h-BN bilayers is observed only for structures with broken inversion symmetry, with an intensity much larger than that of single layer h-BN. In addition, our DF-TEM data identify the formation of interlayer topological defects in h-BN bilayers, likely induced by local strain, whose properties are determined by the interlayer symmetry and the different interlayer potential landscapes. © 2013 American Chemical Society.