Which is better to create 3 related pages? To create for ex. Subfolder1 for main page and Subfolder2 and Subfolder 3 for related pages, or create Subfolder1(index.html) for main page and create Page1.html and Page2.html in this folder? Which will be better for SEO?
Overall, this hardly matters. What matters is the content you are creating, whether it is of interest to people, and whether you add value with it. That said, I would just use a flat site structure because it makes life easier.
Improve your content and see the page design should be appealing and also see that page loads quickly with all target keywords placed as meta tags and meta description and creating folders so that you get additional scope to present your target keywords