The subject of this song is Wilson's wife, Diane, but there is also a lot of pathos behind it, as he asks her to "remove this whirling sadness" and "save me from madness."
"Ever since I was a preteen, I struggled with melancholy and the blues," Wilson explained in a Songfacts interview
where he discussed the song. "My family found my melancholy or my sad side to be very troubling and perplexing. Part of it was that I was a smart kid and I excelled at what I did. I was mostly pleasant. So I was lucky in many, many ways. The path was strewn with roses. My family couldn't understand why these dark moods would strike me for long stretches, but I imagine that's a lot of people's experiences growing up.
It lasted through my 20s and probably into my 30s, so when I wrote 'Secret Smile,' I may have just been experiencing exactly what the song is about. I can't really analyze it, because the lyrics mostly came from a dream and then the rest of it I just tried to channel my intuition rather than thinking intellectually about what the words were going to be."