I conducted a research's project with a Professor at a US University, however it was unofficial. I want to submit the research paper, and I was not sure if I could put my high school as my affiliation or the university which the professor I conducted research with. It was online, and I am not sure if this could make a difference.
First and foremost, I would suggest discussing this with the professor, who will certainly be a co-author on the paper. It may be that your affiliation with the university was more official than you thought it was, and that the professor feels that it is appropriate for you to use it as an affiliation.
If not, however, there is absolutely nothing wrong with listing a high school as an affiliation. I have published with high school co-authors before, and we simply listed their academic affiliation as their high school, since that's the simple honest truth.
Bottom line: a high school as an affiliation is statistically unusual, but entirely proper.