The Windows system partition contains everything that you see when you open your C: drive in Windows Explorer: Windows system files, documents, user accounts, etc.
When you encrypt the system partition, all those files get encrypted with whichever algorithm you choose.
Anyone who gets a hold of your computer will be completely unable to access anything on the C: drive because it's all been encrypted.
HOWEVER, they would be able to access it if your computer gets stolen while it's powered on or in sleep mode (if it's a laptop)
So if you're really paranoid, you should always shut down your system when you're in a situation where it could possibly get stolen.