I used godot engine to make game for a while (3+ years) , and i just want to learn how it work underneath the hood.
I am currently in my third year of university majoring in computer science, so i have some knowledge about computer architecture, system design analysis, oop,… I really want to do my graduation project on game engine based on godot engine.
Is there any reference material?
Godot is already a game engine, no one builds a game engine on top of another game engine. Godot is created using C++.
Here is the link to the source code: GitHub - godotengine/godot: Godot Engine – Multi-platform 2D and 3D game engine
This is good advice to go through the source code, you are lucky that Godot is very legible. Though making a game engine is a very difficult task, focus on making a game without an engine instead, using some basic frameworks like SDL2, GLFW, or Raylib.
I will say there are game engines made in even Godot specifically, RPG in a box is made in Godot 
a really great thing about godot is how easy it is to build.
adding modules to godot is really easy too this really helped me learn how to do that.
this is a lot of info about GDscript
a concept I find interesting in all game engines is the engine loop, the thing that makes the func _process(delta: float) -> void: work. the whole thing is looping all the time. then game devs inject into this loop with the things they want to do. I did not study CS so maybe it’s not really that unique of a concept.
If Godot code-base looks overwhelming in terms of size, you can also consider starting from a smaller, younger code-base such as WickedEngine