A pump housing structure of a three-axis multi-stage Roots pump is provided, comprising a first-stage pump housing, a second-stage pump housing and a third-stage pump housing, wherein the first-stage pump housing is provided with a first center axial hole, a first left axial hole and a first right axial hole; a fixed bearing end cover is mounted on the side of the first-stage pump housing, three fixed bearing chambers are provided on the surface of the fixed bearing end cover; the second-stage pump housing is provided with a second center axial hole, a second left axial hole and a second right axial hole, the third-stage pump housing is provided with a third center axial hole, a third left axial hole and a third right axial hole, and the end surface at the outer side of the third-stage pump housing is fixedly mounted with a non-driving end bearing end cover. The present invention can accommodate and fix three axes through three fixed bearing chambers, respectively. Moreover, since the sum of the axial lengths of the second-stage pump housing and the third-stage pump housing is equal to the axial length of the first-stage pump housing, it not only can strengthen the center stiffness of the three axes of the Roots pump, but also can ensure that the total axial expansion is evenly divided, reducing the cumulated amount of thermal expansion at the end of the axis.