The differences between 3-pin and 4-pin CPU fans are significant in terms of functionality and control. A 3-pin CPU fan has three wires connected to the motherboard. The first wire is for power supply, which provides the necessary electrical energy to make the fan spin. The second wire is the ground wire that completes the electrical circuit. The third wire is the tachometer wire. It sends a signal back to the motherboard about the fan's rotational speed. So, the motherboard can only monitor the fan's speed and detect if it is working or not. It can't actively control the fan speed in a sophisticated manner.

In contrast, a 4-pin CPU fan has an additional wire, which is the PWM (pulse width modulation) wire. This allows the motherboard to have precise control over the fan speed. The motherboard sends a PWM signal to the fan. This signal rapidly turns the power on and off. By adjusting the percentage of time the power is on (duty cycle), the motherboard can control the average voltage supplied to the fan and thus its speed. For example, if the CPU temperature is low, the motherboard can set a low duty cycle, reducing the fan speed and noise. If the CPU temperature rises, the motherboard can increase the duty cycle to speed up the fan and improve cooling. In terms of compatibility, a 3-pin fan can usually be plugged into a 4-pin header on the motherboard, but the PWM control will not be utilized. A 4-pin fan can be plugged into a 3-pin header, but it will run at a fixed speed or be controlled based on the motherboard's basic fan speed settings rather than the more advanced PWM control.