It was necessary to monitor liquid level in both mixing fertilizer tank and recycle tank respectively to design the integrating equipment of water and fertilizer in the intelligent hydroponic control system for facility vegetable production. In practical engineering project, the liquid level floater is widely used for the existing liquid level detection. The effect of the floater can be disturbed by some conditions, such as waterlines fluctuation when the floater was too close to inlet or outlet. Shaking up and down of the floater result in pump to start and stop intermittently, which will damage the pump with great starting current. To solve these problems, the counter was used to design digital filter circuit and MCU timer interrupt respectively in the hardware and software. In order to test the performance of the new intelligent liquid level switcher, the comparison experiments of different depths, pressures and water flows were carried out under the same conditions. The results show that this method can effectively filter out interfering signal. When both the charging resistance and discharge resistance of the counting pulse generating circuit are 4.7 kΩ, the filtered signal delayed 2.11 s after the fact output signal. The effective output signal was cleared off disturbing signal under 2 s by digital filter circuit and kept high stability. The delay time is related to the counting and pulse generating circuit, so different disturbing signals can be declined by configuring filter plus width in circuit design. On the way of software design, timer programming method was used in microcontroller considering width of the wave curve to detect the status of ports at certain intervals. The algorithm was introduced to remove disturbance and improve the efficiency of SCM. The method can be used to filter out the interference signal by setting different values according to the actual situation, such as different power pumps so the smart switcher can be more feasible.