How to set the desktop to $HOME/Desktop?

Create a new folder that you want to use as your folder.

For example, type mkdir ~/Desktop in a terminal (Ctrl+Alt+T to open one) to create a folder named Desktop in your home directory.

Edit your configuration.

Edit the file ~/.config/user-dirs.dirs. You can do this by opening a terminal, then enter:

gedit ~/.config/user-dirs.dirs

Change the entry for XDG_DESKTOP_DIR to your new desktop folder, or add it, if the entry does not exist. After your edit, the file should look like this:

XDG_DESKTOP_DIR="$HOME/Desktop"  
XDG_DOWNLOAD_DIR="$HOME/Download"  
XDG_TEMPLATES_DIR="$HOME/Templates"  
XDG_PUBLICSHARE_DIR="$HOME/Public"  
XDG_DOCUMENTS_DIR="$HOME/Documents"  
XDG_MUSIC_DIR="$HOME/Music"  
XDG_PICTURES_DIR="$HOME/Pictures"  
XDG_VIDEOS_DIR="$HOME/Videos"

Log out and then log in again and your desktop should show the specified folder.