Sometimes we face a problem with the site collection administrators that disable them from login to the site.
I do have a good solution for such problem, the secret is behind the application pools on your server.
first navigate to IIS Manager, and select application pools from left corner.
Then select the web application that contains the site collection which you couldn’t login to.
As you see below select advanced settings…
After that you will see a panel of properties look at the Identity property, you should see your user name (DOMAIN\user name).
make a selection to this name you will see a browsing button click it and you will be prompted to set a new account, write again your domain username and password like below, click ok to close.
Now,only one step remaining just stop the application and restart it again, try to login again, you will be succeeded.
These kind of problems may occur as a result of changing the domain user password, specially if this user is the site collection administrator.