Although the game of Ys Origin itself will work with Xinput (i.e. Xbox 360, Xbox One) controllers, the configuration tool is a separate executable and doesn't seem fully compatible with Xinput. It will not detect button presses for these controllers on Windows 10. This means you can not remap gamepad controls through the config tool and I personally found the default button layout terrible because it was clearly based on a generic gamepad with a different button arrangement.

Luckily, you can edit the controls by editing the config file directly.

1. Open a Windows file explorer window; shortcut: Windows key + E
   
   
2. Paste the following into the "address" bar at the top and press enter:
   %userprofile%\Saved Games\FALCOM\yso_win
   
   
3. This will open the folder where the config file resides. Double click yso_win.ini and it should automatically open in Notepad.
   
   
4. Scroll down to the bottom and find a section of the file that looks like this:
   
   Assign{PAD_ACTION}="Button1" Assign{PAD_JUMP}="Button2" Assign{PAD_SHOT}="Button3" Assign{PAD_USE}="Button4" Assign{PAD_MENU}="Button10" Assign{PAD_WALK}="Button9" Assign{PAD_SWORD_REVD}="Button5" Assign{PAD_SWORD_REVU}="Button8"

That section is where the gamepad buttons are assigned. You just need to edit the button numbers to change the controls. The control names are mostly obvious, except for these:

PAD_SHOT = Use Magic
PAD_USE = Use Boost
PAD_SWORD_REVD / REVU = Previous / Next Skill

The buttons on an Xbox 360 or One controller correspond to the following button numbers:

A = Button1
B = Button2
X = Button3
Y = Button4
LB = Button5
RB = Button6
Back (360)/View (One) = Button7
Start (360)/Menu (One) = Button8
Left stick click = Button9
Right stick click = Button10

The triggers are not remappable because they are analog inputs and not buttons.

So, for example, if you wanted to make the action (attack) button to be the X button instead of A, you'd change this line:
To this:

This layout is based on the default button mapping in the PS4 version of the game, but obviously feel free to change this to whatever you prefer.
This translates to:
Attack/Ok = X
Jump/Cancel = A
Use Skill = B
Use Boost = Y
Menu = Start/Menu
Walk = Left stick click (pointless, never any need to walk)
Previous/Next Skill = Left/Right bumper

The only annoying thing is that you can't remap Ok and Cancel separately from Attack and Jump. Ok must always be the same button as Attack and Cancel must always be the same as Jump. This makes navigating the menu awkward since it makes X the Ok button and A the Cancel button. It's not ideal, but you'll get used to this after time and this layout is much better for the "action" part of the game