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What you are likely hearing is called "alternator whine" and it's a result of the fact that the alternator output isn't smooth but consists of a full-wave rectified AC voltage that varies a few hundred milli-volts. The frequency of the AC is tied directly to how fast the alternator is spinning (i.e. engine revs): higher revs == higher frequency.

The problem is that your installation isn't rejecting this "noise". There are many possible reasons, but some of the most common ones include:

- poor system ground layout. You need to make sure that all components (except speakers of course) are grounded to the same physical point on the car. Distributed grounds (i.e. your head unit is grounded to the OEM stereo ground circuit, the amps are grounded to the trunk floor, the crossover is grounded somewhere else etc) can lead to what are called "ground loops" where the ground potential at each point is not the same: current flows between these grounds, affecting the components' ability to deal with common-mode noise.

- poorly run power cables
Keep power cables from high-noise, unshielded circuits like fuel injector wiring, ignition wiring etc. When an injector shuts off, it can generate a voltage spike of 50V or more, which generates a field around the wire. Any adjacent wires will pick this field up, much like an antenna works, and noise will get into that circuit.

- poor amplifier design
Cheapo amps will have cheesy power supplies that don't have very good "line regulation" (i.e. maintaining consistent voltage output as the input varies). These cheesy supplies' outputs will vary to some degree as the input does, resulting noise in the audio stages. Also, these same amps might have poorly designed audio inputs stages that don't have very good CMRR (common mode rejection ratios) meaning any noise on the audio (picked up from, say, noisy PCM wiring...) gets into the speakers.

You can try "filters" - usually big-ass capacitors and inductors on the power input to your power input to the amps but I doubt it will help much. The size of the components required to form a multi-pole filter with a 3dB point such that you are rolling off at such low frequencies are truly huge, so they aren't that practical. Those cheesy things you get at Radio Shack are absolutely useless.

You can try system isolators that attempt to link the audio input/outputs with, say, fiber optics, with each stage then free to be powered differently but these are expensive.

Have your alternator tested. A blown diode in the rectifier bridge can really affect the noise level produced but not dramatically affect alternator performance.

First thing though is to carefully map out how you've got the system grounds laid out.
 
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