It's built as a full 3D game, and has extensive use of nice shaders for transparency effects like the crystals, water effects, particle effects, and more. This is all pretty standard game development stuff, you'd be able to do this pretty quickly with an off the shelf engine like Godot, Unity, or Unreal. Godot is a good place to start if you want to learn some of this stuff!
However Order of the Sinking Star is also made in a custom programming language and custom engine. This is not at all normal for game development. There also doesn't appear to be a scripting system. Normally you have an engine built in C++ or something fast, and then a scripting system where you write a higher level language to script how the game runs. Engine development is more separate from scripting development. With Order of the Sinking Star, the game engine appears to be much more just like a library, and the same codebase runs the engine and game logic, with no scripting layer, as far as I can figure out from public hints.