- The Site Collection is the root site of the web site.
- A site collection consists of a top-level site and its subsites.
- It is a logical unit for administration - there are settings that can only be configured at the site collection level (in other words, at the top-level site).
Site (SPWeb)
- Must belongs to a Site Collection.
- A Site can contains sub sites.
Web Application (SPWebApplication)
- Just a web application in IIS
- Each Web application can host many site collections.
- A web application needs to have at least one Site Collection
Reference: