The invention relates to the field of large air separation centrifugal compressors, in particular to an assembly method for a rotor with an oversized and overweight three-section type main shaft. Theassembly method includes the step of assembling the three-section type main shaft. Assembly of the three-section type main shaft comprises the steps that a middle section shaft with axial stopping openings in the two ends is subject to coarse machining, and a left section shaft with an axial stopping opening in one end and a right section shaft with an axial stopping opening in one end are subjectto coarse machining; the stopping openings of the middle section shaft, the left section shaft and the right section shaft are subject to finish machining; an outer circle between the left section shaft and the middle section shaft and an outer circle between the middle section shaft and the right section shaft are subject to finish machining, and then a positioning face is formed; and the assembled rotor is subject to high speed dynamic balance testing. By means of the assembly method for the rotor with the oversized and overweight three-section type main shaft, the requirement for the coaxiality of the oversized and overweight three-section type main shaft after assembling is met.