The invention discloses a low-voltage distribution network user topology estimation method and system based on mutual information, wherein, the method comprises the following steps: step S1, obtaininguser voltage time series data and transformer voltage time series data; step S2, obtaining user voltage time series data and transformer voltage time series data. 2, calculate mutual information between user voltage and mutual information between user and transformer accord to time series data of user voltage and time series data of transformer voltage; Step S3, according to the mutual information between the user and the transformer, the user phase identification is carried out according to the K-means clustering algorithm; 4, construct a topology model; Step S5, the topology estimation is completed according to the mutual information between the user voltages by using the minimum spanning tree algorithm for the user after the phase identification. Compared with the prior art, the invention does not rely on the known topology, does not need additional carrier wave, is not affected by the load of the distribution station area, has no field test wiring problem, does not exist securityhidden trouble, and improves the speed of topology estimation.