In order to analyze the shear lag effect of a variable cross-section continuous box girder bridge, a box girder element with 2 nodes and 4 degrees of freedom was selected. The initial parameter solution of the shear lag control differential equation was introduced, and the stiffness matrix and equivalent node load of the box girder segment element were derived. Using FORTRAN language to write corresponding calculation programs, the program was applied to verify a simply supported box girder, and the shear lag effect of a three span variable cross-section continuous box girder bridge under lane load on the main span was analyzed. The results show that the shear lag effect has the greatest impact on the mid span at 1/2, and has almost no effect on the left and right spans; The total deflection at 1/2 of the mid span is 1.08 times that of the elementary beam deflection.