The invention discloses a filling method for lightning stroke missing data of a transmission line. The filling method is used for solving the problem of lightning stroke frequency data missing of the transmission line. The method includes the steps that firstly, weather information is mapped on a number field, mapped numerical values serve as weather impact factors to be added into lightning stroke panorama data, a lightning stroke data set is divided into multiple data sub-sets through the weather impact factors, the mapping relation between the weather impact factors and the lighting stroke frequency is established, and the missing lightning stroke frequency data is estimated through the missing data filling method based on a regression equation according to the cross correlation and mean values of sub-set elements where the missing lighting stroke data is located. The estimated result error of the missing lightning stroke frequency data is small, the problem of lightning stroke frequency data missing is effectively solved, and the powerful data support is provided for lightning stroke fault analysis and lightning-shielding design of the transmission line.