Do any of the following:
Delete large messages or messages with attachments, or IMAP accounts, be sure to download the attachments first—attachments are deleted from the mail server and can’t be retrieved.
Empty your Trash mailbox. Messages you recently deleted are in the Trash mailbox but haven’t yet been removed from the mail server. Choose Mailbox > Erase Deleted Items, then choose to remove them from all accounts or a specific account.
For Keep mailboxes from getting too big in Mail on Mac