Yes, that is Evrai, the Grand Church of St. Eva. There are a total of two assaults on that place in the game, the first is probably the point in the game at which you are at.

If you've already done the inside of the Tree, that means you've received the Bolster Pillow from the Tree. After you have the pillow you need to go to Tunland and use it to shrink and enter the queen's body.

The game really shines at the end. That's where the story unfolds, and it is simply a remarkable experience I have never had duplicated on the SNES. A certain sermon in the Grand Church is one of my favorite video game scenes of all time. Amazing what such an archaic game can do.