The system partition is the primary partition that is used as the active boot partition. System partition must be located on the disk where the computer boots from. One disk can only have one active system partition. System partitions refer to disk volumes containing defined files for the boot of Windows. Files such as Ntldr, Boot.ini, Ntdetect.com, bootmgr and BCD. Under Windows, this partition cannot be formatted.
The Boot partition is the partition where Windows is installed. It includes a Windows directory. Similarly with system partitions, under Windows, this partition cannot be formatted.
A single partition may be both a system and a boot partition.