I bought second hand a audio shelf system RCA model Rs2020. When I put in a cd the speakers make craking noise and it dose it when the sound is louder on the tuner mode.

Try with another speaker, if it still does it, inside repair will be necessary.
Is returning it an option?

I bought second hand a audio shelf system RCA model Rs2020. When I put in a cd the speakers make craking noise and it dose it when the sound is louder on the tuner mode.

Did this happen suddenly? Or is this a new unit and has it been doing this?

CAREFUL WHEN TESTING OTHER SPEAKERS! Make sure the impedance matches and that you do not crank the system to the max. The impedance should be printed on the back of the speaker and the back of the system.

Many shelf systems run at 4 or 6 Ohms where many speakers run at 8 Ohms.