A safe following distance estimation system and an estimation method thereof are provided. The safe following distance estimation system adapted for an autonomous vehicle includes a sensor and a processor. The sensor senses an adjacent vehicle to generate first sensing data, and senses the autonomous vehicle to generate second sensing data. The processor estimates a first friction parameter between wheels of the adjacent vehicle and a pavement according to pavement material data, and estimates a second friction parameter between wheels of the autonomous vehicle and the pavement according to the second sensing data. The processor calculates a safe following distance between the autonomous vehicle and the adjacent vehicle according to the first sensing data, the second sensing data, the first friction parameter, the second friction parameter.