Site structure refers to the way that a site's content - its applications, text, images, videos, music, and more - is grouped, interconnected, and presented to human and non-human visitors.  It establishes the order in which content is discovered, accessed, interpreted, and used.
Think of it like you would a restaurant menu. You want people to get oriented quickly and to enjoy the experience of navigating the menu and deciding what they want to order. You don't want to overwhelm them with too many options at once. Instead, it is better to ease them in gently with selections laid out hierarchically, in a limited number of logical categories and subcategories. Appetizers go first, then main courses, salads, and desserts. No surprises. It is easy for visitors to quickly find what they came looking for and get on with their life.