To change the default file manager in Linux edit /usr/share/applications/defaults.list

$ sudo nano /usr/share/applications/defaults.list

Then search for “inode/directory”. In nano, press Ctrl-W to search.

It should look like this:

inode/directory=pcmanfm.desktop

Change the part after the equal sign to whatever file manager you prefer such as nautilus, thunar, nemo, dolphin, or pcmanfm. You’ll need to have the file manager you choose installed and a corresponding valid .desktop file in the /usr/share/applications directory.

inode/directory=nautilus.desktop

A guide on the Community Ubuntu Documentation for changing the default file manager also recommends setting the value of “x-directory/normal” as well.