how important is movitation in applying for Ph.D. program in physics

Besiding describing my coursework and research experience, I'm wondering whether I should metion more about my motivation for pursing a PhD in physics.
I was enrolled in the school of engineering in the first year due to my country's quota policy in university admission, although my career goal is always to to be a physicist. Ranking first in the end of my first year, I transfered to the physics department.

I want to mention this in my personal statement to show my motivation. But it worries me that whether this will cause misunderstanding. As it may make me seem to spend only three years in the physics department, although I took all the courses in physics.

I think you should rephrase this experience a bit.
Instead of
"Ranking first in the end of my first year, I transfered to the physics department"

you can write something like this
"I worked hard and ranked first at the end of first year so that I could transfer to the Physics deprtment".

According to me that should be fine as it will show you are both hard working and motivated, the two most important qualities required for doing Phd.

This sentence is excellent. I know you are just including it to explain the situation to us, but I think it is a great sentence to include in the essay. It lets the reader know you and your situation. It is so impressive that you did a mech.engineering program and went to the top of the class. I do not think it will reflect negatively on you that you did only three years of physics, because they will see all the physics classes on your transcript.

In answer to your question, I think motivation is the most important quality of the essay. You show motivation by specifying areas of specialization and research interest that appeal to you and also by telling details about your goals for the next two years.

:-)