This guide will let you know how to fix The USB Gamepad Controller Not working in Cemu Emulator.
The first thing you have to do is open Cemu Emulator, then click on options from the top and tap on input settings. Under controller 1, you have to set the Emulated controller to Wii U pro Controller and you will find the Gamepad controller option in the controller drop-down menu.

If your issue is not fixed, then you have to close the input settings and click on Help from the top. Click on “check for update” from the drop-down menu as it will install the latest version of the emulator. After the update, you have to restart the emulator.
Now you have to go to the location where you have installed this emulator and navigate to the controller profile folder. In this folder, you will find one file, you need to right-click on it and then tap on Delete. After this, go back to the main folder of the emulator, right-click on the settings folder and then click on Delete.

After that, open the emulator and then click on the options. Go to the general settings and then click on the Browse button under the MLC path. Go to the emulator folder, navigate to the cemu_1.25.6 folder, and then go into the same folder. You have to select the mlc01 folder and this folder will be added under the MLC path.

Open the Cemu Emulator, click on options from the top, and then tap on input settings again. Under controller 1, you have to set the Emulated controller to Wii U pro Controller and you will find the Gamepad controller option in the controller drop-down menu. You will find your controller option and then you have to click on add. Now you can map your keys. For this, you need to go to the columns in front of the alphabet and then press the buttons on your controller.
