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It tells SpeedFan to control the fan speed according to the rest of the configuration settings.
On the main SpeedFan window, you may have noticed a checkbox for “Automatic fan speed”. However, checking it is not enough to properly set it up, though it would be nice if things were this easy! For now, you can check it, but nothing will happen – you shouldn’t notice any change in your fans’ speeds.
Quick summary:
Temperatures can be influenced by the various fan speeds in your system.
You need to link the fan(s) to specific temperature sensors.
You need to configure the threshold temperatures (when the fan will start working).
The desired temperature tells SpeedFan what it should aim for. Once the desired temperature is reached, SpeedFan will begin to drop fan speeds down to some minimum you specify; if the temperature is above desired fan speeds will increase by an amount related to how much the temperature is above the desired. Once the temperature reaches the warning value, fan speeds will be set to maximum. (100%)
Source Using SpeedFan to automatically control your PC’s fan speeds
The above link explains in detail how to configure SpeedFan correctly.
Thanks for the above link. It made me understand why, despite I have set up an "advanced fan control" configuration, I was getting an unexpected 100% fan speed at a certain temperature threshold. (the SpeedFan interface is a mess, seriously) – Gras Double – 2020-01-25T17:08:17.093