The boss is extremely easy with only 13000 HP and it is weak against Thunder attacks. Have Reimu cast the barrier to block off the death effect.
Have Byakuren enchant Thunder element on Youmu/Sakuya's weapon.
If you want to be safe, use Nitori as commander and use her 3-bomb ability to invalidate one attack. If Youmu is fully geared, you can beat the boss in just 2 turns.
using aya's 3bombs commander skill
Byakuren enchant Thunder element on Sakuya and then using sakuya's private square. repeat the loop again. then you can kill the boss easily without recieve any attack.