Site structure is the set of choices behind how your website is organised: what each web address (URL) looks like, which pages link to which, and whether a section sits on a subdomain (blog.example.com) or in a folder (example.com/blog/).
Google documents some of this precisely, such as the rules for a crawlable URL and for links it can follow. On other parts it says plainly that the choice is yours. This guide helps you review a sample of your own site against the documented parts, and record your decisions on the rest.