The invention belongs to the technical field of medium-low speed maglev traffic engineering low-set lines and discloses a medium-low speed maglev single-line filling section independent pier stud type rail bearing beam transition section structure. The transition section structure comprises pile foundation bearing structures, reinforced concrete rail bearing beam base plates, reinforced concrete beam type structures, lower roadbed filler of a rail bearing beam, two-side backfill filler of the rail bearing beam, a bridge abutment, a trapezoid filling body and end walls, wherein one end of each reinforced concrete rail bearing beam base plate is arranged on the bridge abutment in an overlapping mode, and the end walls are arranged on the two sides of the end, arranged on the bridge abutment in the overlapping mode, of each reinforced concrete rail bearing beam base plate respectively. The transition section structure is higher in long-term stability, the high requirement for rail bearing beam structural deformation and post-construction settlement is met, and the requirement for long-term stability, durability and construction quality controllability of a foundation bed is met. By arranging the end, close to an elevated bridge, of each reinforced concrete rail bearing beam base plate on the bridge abutment in the overlapping mode, smooth transition between a maglev elevated structure and a low-set line transition section F rail is effectively achieved.