The invention relates to an automatic control mechanism of a skin-residue separator for tomatoes. The automatic control mechanism comprises an overflowing device, a liquid level detecting device, a liquid level adjusting device, a controller, a feeding pipeline and a discharging pipeline, wherein the overflowing device comprises an overflowing groove, an overflowing groove driving device, a sliding groove and a settling chamber; the liquid level detecting device is arranged at one side of the settling chamber and comprises a liquid level box and a liquid level sensor; the liquid level sensor is arranged in the liquid level box; the liquid level adjusting device is connected with the settling chamber by a water pumping pipe, a water supplying electromagnetic valve and a water supplying pipeline and comprises a water storage pool, a water pump, a water source pipeline, a flow returning pipeline, the water pumping pipe, the water supplying pipeline, the water supplying electromagnetic valve and a flow returning electromagnetic valve. The automatic control mechanism has the advantages that the liquid level of the settling chamber for separating skins from residues of the tomatoes is automatically adjusted by the overflowing groove, and is detected in real time, and the switching on and off of the flow returning electromagnetic valve and the water supplying electromagnetic valve are controlled to adjust the flow rate of the overflowing groove, the separating rate and the separating purity of the skins and the residues are improved and the overflowing loss is reduced.