The invention discloses a system side harmonic impedance estimation method and a system based on a variance minimum criterion, and the method comprises the following steps: S1, carrying out the sampling at a common connection point, obtaining sampling data, and carrying out the segmentation of the sampling data according to hour segments; wherein the sampling data comprises a current value and a voltage value; wherein the hour segment is a time segment of which the length is less than 10% of the total length of the sampling data; S2, establishing a system side harmonic impedance variance minimum function for the segmented sampling data according to a variance minimum criterion; S3, solving the variance minimum function according to a matching method, and obtaining system side harmonic impedance; the system comprises a sampling unit, a segmentation unit, a construction unit and a solving unit. According to the method, it is assumed that the harmonic impedance change rule during actual operation of the system is met, the harmonic impedance change can be tracked within an hour period, and compared with a traditional method based on the assumption that the harmonic impedance of the system is not changed, the changed system impedance is estimated more accurately.