The invention discloses a distribution line loss diagnosis method and system based on multi-source penetration correlation. Same-period line losses need penetration correctness of data transmission and correlation between different systems; and the line loss abnormity can not be searched easily and much time is spent. The method comprises: state data consistency checking is carried out on data ofa multi-source data set; data are obtained by the multi-source data set, data are transmitted by using an effective link of a source terminal service system, and a distribution multi-source distribution penetration diagnosis is realized based on determined forward and reverse penetration diagnosis rules; a high-loss distribution line is obtained by a line loss index abnormity threshold and a two-dimensional correlation analysis is carried out to diagnose the distribution line index abnormity dynamically; for the high-loss distribution line, a line loss rate influence cluster analysis is carried out; and with integration of the multisource distribution penetration diagnosis result, the comprehensive correlation analysis diagnosis is carried out on the grid line loss based on a static physical relation factor and a dynamic statistic factor that affect the line loss, so the positioning abnormity problem is solved and the line loss management level is improved.