That is not a good idea at all.
The fan plugged into the CPU_FAN header is governed by a temperature sensor inside the CPU chip, so THAT fan ONLY is trying to make sure the CPU internal temperature is OK. BUT what you've done is get the CPU temperature to control the case ventilation. Meanwhile, the actual CPU cooling fan is now under the control of a different sensor in the middle of the motherboard. That's wrong!
The real problem needs to be solved. It appears your CPU_FAN header's automatic control system is sending out signals to its fan that try to run it so slow that the fan actually stalls. That VERY likely means you need to adjust the way the CPU_FAN header is configured. BUT before you do that, tell us something else. Have you added into the wires for that CPU cooling fan a little thing called a "Low Noise Adapter"? THAT can be a real problem if you did. If not, OK, we'll proceed.
Post back here the exact maker and model number of the CPU cooling fan. If it was the one that came with the CPU chip, tell us that. Then also post here the exact maker and model number of your mobo. With those things we can look up your system and advise precisely what to do.