Mechanical ventilation systems are applied in greenhouses for temperature adjustment, but they consume a large amount of energy. This research aims to optimize the energy consumption of a variable air volume (VAV) fan-pad evaporative cooling system via experimentation. We discuss the effects of adjusting the VAV fan-pad evaporative cooling system on temperature and humidity, and we provide an estimate of the corresponding energy consumption under different highest stable temperature conditions. The test results demonstrate that a higher fan frequency is typically accompanied by greater ventilation quantity, faster cooling speed, more pronounced effects of the fan-pad evaporative cooling system fan, and more intensive energy consumption during the cooling process compared with a low fan frequency. When the temperature increased for 71 seconds or 60 seconds in a specific temperature zone (34 to 35 °C), the indoor temperature could be reduced to the optimum for crops with a fan frequency of 20 Hz, saving more than 87% of the energy output. When the warm-up time for a specific temperature zone (34 to 35 °C) was 41 seconds, the indoor temperature could be reduced to the optimum temperature for crops only when the fan frequency was 50 Hz. The VAV fan-pad evaporative cooling system increased the relative humidity in the greenhouse to satisfy crop production demands. The temperature of crops shared the same variation trend as temperatures inside the greenhouse. Our research results theoretically benefit cooling control and energy-saving design of greenhouses in the subtropics.