Lithium niobate (LN) single crystals have emerged as one of the most valuable materials for integrated photonics materials due to their exceptional properties, including non-linear and electro-optical effects. Compared to congruent lithium niobate (CLN) crystals, near-stoichiometric lithium niobate (nSLN) crystals exhibit more pronounced non-linear and electro-optical properties, offering higher application value. nSLN crystals with high compositional uniformity can be prepared using a vapor transport equilibration method. However, large-size LN single crystals are highly susceptible to twinning defects and wafer cracks during diffusion processing. Here, large size nSLN single crystals were prepared using the vapor transport equilibration method to address the aforementioned defects and cracking. The twinning defects within wafers after diffusion processing were characterized, the mechanisms of twinning formation were analyzed, the wafer placement method to produce complete 4-inch (100 nm) and 6-inch (153 nm) wafers was modified, and the composition and transmittance of wafers were tested. Results indicate that composition of the wafers is at least 49.94% (in mole), approaching stoichiometric ratio, and their transmittance is greater than 71% across the 600-3300 nm range. Both Z-cut and X-cut wafers prepared by vapor transport equilibration method exhibited twinning defects. However, cracks were observed when twinning defects intersected on Z-cut wafers, whereas no cracks were present on X-cut wafers. The twinning planes on both Z-cut and X-cut wafers were depending on {011¯2}, which they were identified as deformation twins. According to the mechanism of deformation twin formation, the non-uniform deformation of lithium-rich materials is identified as the primary driving force beneath the twin formation. Ultimately, it was proposed to mitigate twin activation by modifying the diffusion treatment process, thereby increasing the yields of 4-inch (100 nm) and 6-inch (153 nm) nSLN wafers.