The invention discloses an offset printing fountain solution self-circulation purification system and method. The system comprises a first water tank, a second water tank, a layered deposition filter, a filter, a third water tank and a control circuit. When through the control circuit, it is found that particle solubility of a fountain solution in the first water tank is less than a preset value, the control circuit controls a 3-way shift switch so that the fountain solution flows into a first chamber, when through the control circuit, it is found that particle solubility of the fountain solution in the first water tank is greater than the preset value, the control circuit controls the 3-way shift switch so that the fountain solution goes through the layered deposition filter, flows into the first chamber, then enters a self-circulation filter system and is subjected to cyclic purification, the control circuit receives signals of a thermometer, a pH detector and a conductivity detector, and when the pH and the conductivity are higher than a corresponding pH threshold and a conductivity threshold, alcohol and water are added into the primary fountain solution according to a certain ratio. The system and method have high fountain solution purification efficiency, realize real-time accurate detection of indexes of the fountain solution, make the fountain solution quality stable and guarantee printing quality.