I want to say that, I liked my job, but because of some personal problems I left it. To do so, is using my inner soul in the the following sentence correct? if not, any suggestion (in formal English)? Despite my inner soul, I had to leave my job and come back to my home town.
It would be unusual to express oneself in that manner in the context of quitting a job, at least in the US. That is not to say you shouldn't do so, only that you would be unusual in expressing yourself in that manner to most hiring committees here. A more mundane way of stating that idea would be:
Although I would have liked very much to continue working there, I had to move back to my home town for personal reasons.
Depending, you could say "my conscience said to move..." if it was a feeling of duty or justice. I expect to leave my current position to help my grand mother live the last years of her life, even though my position is rewarding: My conscience tells me this.
If it was a matter of inability to enjoy life far away (homesickness), it could be "I was not satisfied living there, even though the position in the company was very satisfying."
Or, if it is anything you do not want to disclose, "I had to resign the position and return home for personal reasons". You would not even have to disclose where: "A personal matter might have kept me from meeting professional expectations, so I resigned."
If true, I would be sure to note that you gave them notice of intent to quit as soon as you knew it had to happen. Similarly, if you were able to assist your boss(es) in getting things ready for your successor, state that. Sometimes people think the phrase "personal problems" is used to hide irresponsibility. If you can show that you were conscientious until you turned in your key that will suppress alot of that speculation.
Total aside: I had to leave a position once and it was a mess. I did get through the problem and come out the other side. Not the same, but not crippled either. I hope you do to.
In English, like many other languages, the metaphorical organ for deep personal feelings is the heart. We might say something like:
I feel in my heart that this is the right decision
It is my heartfelt wish that you will be successful.
I congratulate you from the heart.
In your case, you might say something like:
Although I really wanted to stay at that job, I knew in my heart that I had to return to my home town.
Or the other way around:
Despite my heartfelt desire to stay at that job, I was obligated to return to my home town.
There are many idioms with soul, but those that relate to this kind of context refer to your deeply personal thoughts and memories rather than desires:
I want to bare my soul to you, because I feel I can trust you.
Although in some cases they can refer to a kind of spiritual peace
Confession is good for the soul
Combine with heart and you get an effort of both body and mind:
Although I put my heart and soul into this job, I had no choice but to go back to my home town.