That's not a question on WinSCP in the first place. Ask Godaddy support.

Hi,

I have setup cloud server, and I need to know that how to login in ftp with root, when I login with user+pass of created server, it gives me error permission denied.

Please help me.

You better follow the advice in the "Direct login" section:
https://winscp.net/eng/docs/faq_su

Using Godaddy Cloud
Can access Root only by login as Cloud user + pass
then typing "sudo su -"

Need to access "Root: from winscp


Add a line to your sudoers file:
Cloud user ALL=NOPASSWD: /usr/libexec/openssh/sftp-server

Then in the SFTP setup section of WinSCP edit the session SFTP server:
sudo su -c /usr/libexec/openssh/sftp-server

However when I start winscp /w Cloud user + pass
I just loops and close

Am I missing something?