Here is the full list of all 16 Ys VI: The Ark of Napishtim achievements. It takes around 15-20 hours to unlock all of the achievements on Windows.
Win a boss fight with 1 HP remaining.
Obtain every other achievement.
Complete Boss Rush mode on any difficulty.
Defeat Majuunun.
Acquire every Tabulas.
Complete the game on Nightmare difficulty.
Complete the game in Catastrophe Mode.
Destroy the Ark’s Central Shaft.
Defeat Ernst.
Acquire all equipment.
Win a boss fight without taking a single hit.
Defeat Orjugan.
Defeat Ud-Meiyu.
Defeat Zonplas.
Win the duel with Geis.
Defeat the Wandering Calamity.