The lowest part is the physical visible body.
On top of that, you have the invisible physical body. That's your biofiled or etheric body.
On top of that you have the mind which contains thoughts and emotions and is itself divided into astral and mental planes.
There is more after that but we'll focus on these three layers for now.
These three aspects of our life are totally interconnected.
The reason why you don't fully see the connection between thoughts and physical body is because you don't fully see the biofield which is the layer of energy in between those two.
http://vitalcoaching.com/biofield.htm