Both fetch your email, but they work differently.

• IMAP keeps your mail on the server and syncs it across all your devices. Read a message on your phone and it shows as read on your laptop too. Best for most people.
• POP3 downloads mail to one device and (by default) removes it from the server. Good only if you use a single device and want a local copy.

Tip: Choose IMAP unless you have a specific reason not to — it keeps everything consistent everywhere. Note that IMAP counts toward your mailbox storage, so empty large folders and Trash periodically.