The invention discloses a DNA methylation site analysis device and method based on a triple helix nucleic acid structure, and the device comprises an analyzer body, a workbench, a damping assembly, a station plate, an antiskid assembly, a sample box, a connection assembly, a protection cover, a triple helix nucleic acid structure photoelectrochemical biosensor, a fluorescence excitation lamp and a touch display screen. The workbench is arranged on one side of the top of the analyzer body, the center of the top of the workbench is fixedly connected with the bottom of a damping assembly, and the damping assembly is composed of a damping plate, a single-end stud, a rubber cushion plate, a limiting nut and a buffer spring. The anti-skid structure is additionally arranged, so that the problem that a sample topples and leaks in the moving process of the device is solved, resources are saved, resampling is not needed, the analysis cost of methylation sites is reduced, and the connecting structure is additionally arranged, so that a worker can conveniently disassemble and assemble the protective part, maintenance and replacement are rapid, the labor intensity of the worker is reduced, and the maintenance cost of the device is saved.