Hi salong'
There are a couple (or combination) of things that could be causing your problem.
First:, how are you feeding the subwoofer's amp. Are you using a "line-out" directly from the hu (RCA's), or "high-level"; taking the signal from the left and right speaker outputs? If you are using the "high level" signal, you may need to include the use of a LOC (line output converter) which helps to match the higher voltage speaker output signal (800mV to 8vdc), with the 'more sensitive', low voltage input requirement (200mV to 2vdc) of the amplifier. My two
jl audio HD-750/1 mono-blocks have an "Input sensitivity selector switch" which does exactly what an loc does; your amp may employ one as well. But a mis-match here could cause a very serious "electro-magnetic field" (emf) hum.
Amazon.com: Boss Audio Systems Car High Level to Low Level Converter (B65N): Car Electronics
Second: Has a proper input sensitivity adjustment been performed after the equipment was installed? This is an extremely important step. To neglect doing this can create excessive distortion, poor/inadequate volume levels, and introduce much electrical noise into the program signal. Here's a link to make things easy if you haven't done this yet:
JL Audio » header » Support » Tutorials » Tutorial: Input Sensitivity (Gain) Setting Take your time w/ this tutorial and be comfortable with it... it's your best friend!
I really liked "Bucket81's" suggestion and link, that'll take care of any poor grounding issues if there are any. One more thing I'd like to mention. Something known as a "ground loop" effect. Since your car uses it's body/frame as an electrical path back to the battery, sometimes "electrical noise" is allowed to travel into your audio system, and amplified through the HU and other audio components. This electrical noise may also include "RF (radio frequency) signals"
This electrical noise can be "filtered" out and routed to a proper ground using a device called a "ground loop isolator". They are very inexpensive and easily installed; here's a link to a good one (check it's reviews):
Amazon.com: Boss Audio Systems Car Ground Loop Isolator (B25N): Car Electronics Hope this helps. Be sure to let us know how things worked out with this and best to you!
rigtec, cheers