After doing some research on this forum, the problem may be one of these: amp rattle, cone rattle or bolt not fasten well. I downloaded some test tones and made an CD to do extense testing. The AVR 's sub gain is set -3dB and sub level at 7 o'clock followed sirquack's advice.
I tried to remove the amp out of the box and placed on the floor and listened. The rattle now sounds louder like motor vibrating with some higher freq. The sound came from the box. Since I am using spike, the sound is similar to that I am moving the box around(it is concrete ground). And I found one loosen spike hanging around. I tried to fasten that spike by hand only and listen again, with the amp placed back.
The rattle seems reduce a lot. I realized that if the ground is not flat there may be vibrating between them.
I am thinking if using rubber feet will be better because if I increased the volume to -20dB on AVR I can still hear some rattle.