The invention provides a comprehensive pipe gallery structure crossing an underground shallow-buried structure. The comprehensive pipe gallery structure comprises one or more standard comprehensive pipe gallery segments, one or more pipe gallery transition connection segments and one or more deformation section comprehensive pipe gallery segments; the standard comprehensive pipe gallery segments and the pipe gallery transition connection segments are connected through deformation joints, and the pipe gallery transition connection segments and the deformation section comprehensive pipe gallerysegments are connected through deformation joints; and the heights of the deformation section comprehensive pipe gallery segments are less than those of the standard comprehensive pipe gallery segments, and the set heights of the deformation section comprehensive pipe gallery segments are greater than those of the standard comprehensive pipe gallery segments, so that the deformation section comprehensive pipe gallery segments cross the underground shallow-buried structure. The pipe gallery transition connection segments and the deformation section comprehensive pipe gallery segments are additionally arranged, by decreasing the section heights of the deformation section comprehensive pipe gallery segments and increasing the position heights of the deformation section comprehensive pipe gallery segments, when encountering the underground shallow-buried structure, the deformation section comprehensive pipe gallery segments are lowered to cross the underground shallow-buried structure, interruption of a whole section of comprehensive pipe gallery is avoided, and operation maintenance by workers is facilitated.