The invention provides a weld box section steel joint multi-scale finite element modeling method. The weld box section steel joint multi-scale finite element modeling method includes: S1, selecting an element type combination used for multi-scale modeling from ANSYS finite element software; S2, performing initial geometric modeling on weld box section steel joints; S3, guaranteeing correct directions in a spatial structure for rod pieces by adjusting direction points of all the rod pieces; S4, deleting redundant portions at intersections of the rod pieces, which run through the interiors of the rod pieces, so as to conform to characteristics of weld sections among all the rod pieces; S5, assigning solid element attributes to one third of the length of each rod piece in a complete geometric model of the steel joints, assigning beam element attributes to two thirds of the length of each rod piece in the complete geometric model of the steel joints, and dividing coarse grids and fine grids so as to obtain a multi-scale finite element model of the steel joints. The weld box section steel joint multi-scale finite element modeling method is provided according to unique advantages of the multi-scale finite element model, assists a structural health monitoring system, obtains local detail information of the weld box section steel joints, simulates structural real behavior, and guarantees structural safety.