Yamato was designed by Keiji Fukuda and followed the trend of unique and generally excellent indigenous Japanese warship designs begun in the 1920s by Fukuda's predecessor Yuzuru Hiraga. The design of Yamato contained a number of unique features, some of which contributed to the striking appearance of the vessel. To begin with, unlike most of the designs of the 1920s and 1930s, Yamato's deck was not flush. The undulating line of the main deck forward saved structural weight without reducing hull girder strength. Tests of models in a model basin led to the adoption of a semitransom stern and a bulbous bow, which reduced hull resistance by 8%.

The nine 460 mm main battery were the largest ever fielded at sea, a major technological challenge to construct and operate. Their successful implementation in the Yamato class constitutes a major achievement on the part of Japanese naval constructors. The exponentially higher blast effect of the main armament prevented the stowage of boats on deck or the stationing of unshielded personnel in combat. As a result, all anti-aircraft positions (even the smallest) were enclosed in blast shields as designed. Later in their career the anti-aircraft armaments of both ships were considerably augmented by open positions of both light and heavy weapons. Presumably, AA gun crews would evacuate the weather deck prior to the firing of the main armament. This might help explain Yamato's ineffectiveness at the Battle off Samar; the ship was under almost continual air attack and may have been prevented from firing her main armament at the risk of killing or disabling gunners in open positions. For similar reasons, the superstructure of the ship was extremely compact, which reduced armored citadel length but also hampered anti-aircraft arcs of fire.