In i3wm, start nautilus will show a desktop, which is useless.
To prevent this desktop showing when starting nautilus,
run gsettings set org.gnome.desktop.background show-desktop-icons false.
To enable it again, run
gsettings set org.gnome.desktop.background show-desktop-icons true
Turning off desktop will make wallpapaer disappear, which makes the desktop looks bad in Unity environment.
Ref:
How to stop nautilus managing desktop in unity
How to disable nautilus from handling the desktop?
How can I get rid of the nautilus desktop window?