In that case the fix involves removing that Account from your Mac, followed by adding it again. That action will not affect any messages that remain undeleted on the server.
Instructions are described in Add or remove email accounts in Mail on Mac - Apple Support. You will be following them in reverse order—in other words, remove the email account, and then add that same account again.
If you are unable to even open the Mail app due to its crashing immediately upon launch, you may not be able to access Internet Accounts from within Mail as it describes. Instead, amend those instructions as follows:
Click the (Apple menu) > System Preferences... > Internet Accounts, select the affected account, and then deselect the Mail checkbox for the account. To stop using the account in all apps, make sure the account is selected, then click the Remove button [—].
Please note that merely deselecting the Mail account won't remove it. It just temporarily turns it off in the Mail app, and selecting it again turns it on again in Mail. You need to follow the last (boldface) sentence above to actually remove the account. Adding it again will cause Mail to repopulate its contents. Since messages that remain on the server will be repopulated, you need to find and delete that message first. That can be accomplished through your email service provider's webmail interface, provided it offers one (most do).
Be advised that if Mail is crashing due to the way a particular message is formatted, Mail's crashing problem is certain to occur when another similarly formatted message is eventually received. Only Apple would be able to fix that, and the likelihood of them doing so with an update to a macOS version as old as "El Capitan" is just about nil.