I have created one SharePoint web application in SharePoint 2013 farm. And that web applications port number is conflicting with the port number of other non SharePoint point IIS site in the application pool of IIS Manager. So if I delete the SharePoint site will it delete all the IIS sites associated with the same port number in application pool. If yes what would be the way to delete the SharePoint web application along with its content database without deleting other IIS sites with same port number in application pool.
So if I delete the SharePoint site will it delete all the IIS sites associated with the same port number in application pool.
No, it's not related to the port it's related to the IIS site itself and its application pool.
but I think the deleting option is not a good solution especially if you already do some work in your web application, so it's recommended to change the port of the SharePoint web application rather than delete it.
The simple way to change the port number of the web application is to extend it to a new web application from central administration, then and provide the new port.
Now you have a new IIS site with a new port with the same content database, and you can now solve the issue of conflicting port easily, eg.by stopping the first SharePoint web application in IIS.