Thanks for that info. I can outline how to configure fan header setting in BIOS Setup. Note that each header is configured separately. I see also that your mobo has only one header of each type: one for the CPU cooler, and one for case ventilation fans.
There is a potential problem here that MAY relate to your issue. Fan motors come in two types. The older design are called "Voltage Controlled Fans" or "3-pin fans". They have three wires in the cable, and the female connector on the end has three holes. It has two ridges running down one side of the connector, and these fit around a plastic "tongue" that sticks up beside the male header pins on the mobo, so you can only plug them in one way. Control of the fan speed is accomplished by varying the VOLTAGE of the power supplied on Pin #2.
The newer design are called "PWM Fans" or "4-pin Fans". These have FOUR wires in the cable and 4 holes in the connector. It looks a LOT like the 3-pin connector, just a bit wider, and the corresponding male mobo header has 4 pins. The method or "MODE" of speed control for these is different. Power on Pin #2 is always the full 12 VDC, and the fourth pin supplies the new PWM control signal. Inside the fan, a small chip uses that signal to modify the flow of current from Pin #2 through the windings to achieve speed control.
4-pin fans were designed with some backward-compatible features so you CAN plug either fan type into either header type. But If you plug a 3-pin fan into a header using the new 4-pin PWM Mode for control, that fan can only run full speed all the time. On the other mis-match, you CAN control the speed of a 4-pin fan using the older 3-pin Voltage Control Mode, although that is not quite ideal. As a result, although you CAN connect fans of both types together to one header, it is preferable NOT to mix this way if you can avoid it.
Almost all mobos now have fan headers ONLY with 4 pins. But the options in BIOS Setup for each header allow you to specify which type or MODE of control system that header uses for its fans.
Now, MODE is the METHOD by which the mobo header exercises control of speed. But DECIDING what speed should be is another choice, the PROFILE. Your mobo has a limited set of options here illustrated in the manual on p. 14. On that screen the graph is a "fan curve" of what speed to run for a range of temperatures. It comes pre-set, but you can change any of the four points on the graph by dragging it with your mouse pointer. For now I suggest you do not make such changes, but you can later after considering other items.
FIRST we'll look at the MODE item for each of your two headers. For the CPU_FAN header I am sure it is a 4-pin fan on that cooler, so at upper left make sure it is set to PWM Mode. Now go to the SYS_FAN header. Often the MSI mobos come with this one pre-configured to DC Mode, but you can check that. What you do want for this is: if both your case fans are 3-pin, set it to DC Mode. If both are 4-pin, set it to PWM Mode. I am assuming here that both of your case fans are connected to the only SYS_FAN header you have by a Splitter.
BUT what if you have something else? For example, it is possible that only ONE of those fans is plugged into the SYS_FAN header, and the other is connected instead directly to a power output from the PSU. In that case there is NO ability to run the directly-connected fan at less than max speed, so we'll need to find a solution for that.
Another possibility is that both fans are connected via a Splitter to that SYS_FAN header, BUT they are different types - one 3-pin and one 4-pin. In that case IF the header is set to use PWM Mode, then the 3-pin fan will always run full speed and make more noise. You can change that. If you set the SYS_FAN header to use DC Mode, BOTH fans will be under speed control and run quieter, even though this is not quite ideal for the 4-pin fan.
So make any changes you deem necessary in BIOS Setp. When done, use the F10 key to pop up a small screen that asks you to confirm that you want to SAVE your settings and REBOOT. Do that. See if that improves your situation.
If that still does not solve the issue, post back here the details. How is the SYS_FAN header configured? How are the two case fans connected to what? Are those two fans the SAME type or different? If the same, which: 3-pin or 4-pin? Can you tell which of your THREE fans is making the most noise?