When your iPhone has been setup for email you can control whether to keep or delete messages received from your webmail or email server
Do the following :-
1. Select Settings on the iPhone
2. Select Mail, Contacts, Calendars
3. Select required Email Account
4. Select Advanced
5. Select Delete from server in Incoming Settings
6. Now Select the required option:-
a) Seven days
b) When removed from Inbox
PLEASE NOTE – You will only see the option to delete from the Server for POP3 Accounts.
If the account is an IMAP account all emails deleted from the Phone also delete from the IMAP server, this is how IMAP accounts are designed to work.