Got from a song-what does “You are my sunshine, my only sunshine . . .” means as it’s actually metaphor?

No. The person that wrote the song was telling the person he loved that she was what made his life happy and bright. It had nothing to do with anyone's son.

You are my sunshine is often called “heartwarming”, but a close look at the lyrics after the first verse shows that they're better described as “heartbreaking”. It's about unrequited love. This song has enjoyed enduring popularity for nine decades.

"You are my only sunshine" means "you're the only thing that makes me happy."

Well it isn't as brilliant as the song Good morning Starshine.  The metaphor better explained in "You twinkle above us We twinkle below"

The compound element "sun" in "sunshine" is not being used to refer to the person that the song's addressing as his "son" because, first of all, the writer of the song, Oliver Hood, had no sons; second of all, he himself said he wrote the song for his first and only girlfriend when she broke up with him, his only girlfriend because she ended up getting back together with him and they got married and stayed married until he died; and third of all, the lyrics make it pretty clear that it's written to the writer's sweetheart, not to his son, with verses like "I'll always love you and make you happy, if you'll only say the same, but if you ever leave me for another, you'll regret it all one day," for that smacks of pederasty as parents don't generally want their children to never leave and get married but always stay with them, but I suppose the writer being a family pederast and having his son for his sweetheart wouldn't be totally outside of the realm of twisted possibilities if not for that one simple fact: the fact that the writer, Oliver Hood, had no sons.

If you want to understand the song's metaphor of calling someone "sunshine," you need only listen to the lyrics. The lyrics provide a clear explanation. It's no mystery. 

It means you make me happy when skies are blue . Solar rays .