According to the deformation characteristics of global side torsion buckling for rectangle thin-walled aqueduct, the critical load of side torsion buckling for rectangle thin-walled aqueduct is deduced by Galerkin method. Influences of prestress and vertical deformation before buckling are considered. The variation rules of critical load are analyzed with four factors: span, flange width, ratio of height to width, thickness. The analysis results show that the aqueduct span is the biggest influence on the critical load of side torsion buckling for aqueduct; for rectangular thin-walled aqueduct, in conventional aqueduct section size and span, its critical stress of side torsion buckling is greater than concrete compressive strength design value , therefore side torsion buckling won't happen in usual aqueduct; if steel with high yield limit is used, stability check calculation must be carried out. Results and conclusions obtained can be referenced for the global stability design of thin-walled aqueduct.