The configuration file for Mupen64plus is /opt/retropie/configs/n64/InputAutoCfg.ini.
$ sudo vim /opt/retropie/configs/n64/InputAutoCfg.ini
Paste this content:
; Generic USB Joystick _START
[Generic USB Joystick ]
plugged = True
plugin = 2
mouse = False
AnalogDeadzone = 4096,4096
AnalogPeak = 32768,32768
Mempak switch =
Rumblepak switch =
R Trig = button(5)
Start = button(9)
Y Axis = axis(1-,1+)
Z Trig = button(7)
DPad U = hat(0 Up)
A Button = button(6)
DPad D = hat(0 Down)
X Axis = axis(0-,0+)
DPad R = hat(0 Right)
B Button = button(8)
DPad L = hat(0 Left)
C Button R = button(1)
C Button L = button(3)
C Button D = button(2)
C Button U = button(0)
; Generic USB Joystick _END