The main difference between 3-pin and 4-pin CPU fans lies in their functionality and control capabilities. A 3-pin CPU fan has three connectors: a power pin, a ground pin, and a tachometer pin. The power pin supplies the electrical power to run the fan. The ground pin provides the return path for the electrical current. The tachometer pin is used to send a signal back to the motherboard about the fan's rotational speed. This allows the motherboard to monitor the fan speed but not directly control it. The motherboard can only detect if the fan is spinning and at what speed.

On the other hand, a 4-pin CPU fan has an additional pin, which is a PWM (pulse width modulation) pin. The PWM pin enables the motherboard to control the fan speed more precisely. The motherboard can send a PWM signal to the fan, which varies the voltage supplied to the fan in a rapid on-off cycle. By adjusting the duty cycle of this signal, the motherboard can control the average voltage and thus the fan speed. This allows for more efficient cooling as the fan speed can be adjusted according to the actual temperature of the CPU. For example, when the CPU is idle and generating less heat, the motherboard can reduce the fan speed using PWM control, resulting in quieter operation. When the CPU is under heavy load and generating more heat, the fan speed can be increased to provide better cooling. In terms of compatibility, 3-pin fans can usually be plugged into 4-pin headers on the motherboard, but the motherboard will not be able to use the PWM control. 4-pin fans can also be used in 3-pin headers, but the PWM control will be disabled and the fan will run at a fixed speed or be controlled based on the motherboard's basic fan speed settings.