Citra的手柄支持相当的烂。。。。但也不是没有办法 官网论坛有解决方法，测试有效
1.找到qt-config.ini 一般是在c:\User\用户名\appdata\roaming\citra\config\
找不到也可以Win+R 输入%appdata%/citra/config/
2.打开qt-config.ini，记事本就行修改[controls]部分 就是下图高亮的部分。根据你自己用的手柄替换成下面的DS4的或者360/XBone的。

3.看你是啥手柄PS4的 DualShock4可以试试下面这段
[Controls]
button_a="engine:sdl,joystick:0,button:2"
button_b="engine:sdl,joystick:0,button:1"
button_x="engine:sdl,joystick:0,button:3"
button_y="engine:sdl,joystick:0,button:0"
button_up="engine:sdl,joystick:0,hat:0,direction:up"
button_down="engine:sdl,joystick:0,hat:0,direction:down"
button_left="engine:sdl,joystick:0,hat:0,direction:left"
button_right="engine:sdl,joystick:0,hat:0,direction:right"
button_l="engine:sdl,joystick:0,button:4"
button_r="engine:sdl,joystick:0,button:5"
button_start="engine:sdl,joystick:0,button:9"
button_select="engine:sdl,joystick:0,button:8"
button_zl="engine:sdl,joystick:0,axis:3,threshold:-0.8,direction:+"
button_zr="engine:sdl,joystick:0,axis:4,threshold:-0.8,direction:+"
button_home="engine:keyboard,code:66"
circle_pad="axis_x:0,engine:sdl,joystick:0,axis_y:1"
c_stick="axis_x:2,engine:sdl,joystick:0,axis_y:5"
如果是XB360或者XBOX One的可以用这段
[Controls]
button_a="engine:sdl,joystick:0,button:1"
button_b="engine:sdl,joystick:0,button:0"
button_x="engine:sdl,joystick:0,button:3"
button_y="engine:sdl,joystick:0,button:2"
button_up="engine:sdl,joystick:0,hat:0,direction:up"
button_down="engine:sdl,joystick:0,hat:0,direction:down"
button_left="engine:sdl,joystick:0,hat:0,direction:left"
button_right="engine:sdl,joystick:0,hat:0,direction:right"
button_l="engine:sdl,joystick:0,button:4"
button_r="engine:sdl,joystick:0,button:5"
button_start="engine:sdl,joystick:0,button:7"
button_select="engine:sdl,joystick:0,button:6"
button_zl="engine:sdl,joystick:0,axis:2,threshold:-0.8,direction:+"
button_zr="engine:sdl,joystick:0,axis:5,threshold:-0.8,direction:+"
button_home="engine:keyboard,code:66"
circle_pad="axis_x:0,engine:sdl,joystick:0,axis_y:1"
c_stick="axis_x:3,engine:sdl,joystick:0,axis_y:4"
4.疑难杂症的不是上面的手柄的可以先试试XboxOne的那段，不行的话去这里找找

看看有没有你的手柄。