The invention discloses a supercritical carbon dioxide axial flow compressor and axial flow counter-rotating turbine double-shaft structure. The structure comprises an axial flow compressor, an axial flow counter-rotating turbine, a load and a heater; the first output end of the axial flow counter-rotating turbine and the axial flow compressor form a coaxial structure through a low-pressure shaft; the second output end of the axial flow counter-rotating turbine is connected with the load to form a coaxial structure through a high-pressure shaft; a working medium outlet of the axial flow compressor is connected with an inlet of the heater, and an outlet of the heater is connected with a working medium inlet of the axial flow counter-rotating turbine. By adopting the novel structure, the structure is small in size, simple and compact and has higher efficiency; the overall resultant force moment of the structure is reduced due to counter-rotating of a rotary shaft, and therefore the safety and stability of the structure are improved.