In view of the current situation of manual operation, low efficiency, unstable assembly quality and many potential safety hazards in the docking assembly of various conical flying body sections in China, an automatic flexible docking mechanism for the docking of conical flying body sections is designed. Accord to that different conical sections of the product, the mechanism adopt a multi-degree-of-freedom platform as a support, uses an attitude measurement algorithm to carry out position and attitude detection and docking attitude planning on different doc sections, and meets automatic flexible docking assembly between different conical sections, wherein the relative accuracy of displacement adjustment reaches 0.01 mm, and the relative accuracy of angle adjustment reaches 0.01 degree. The results show that the mechanism can effectively improve the assembly efficiency and assembly quality of the flight body, eliminate the potential safety hazards of assembly, fill the gap of the intelligent docking assembly technology of the conical flight body section in China, and meet the needs of the rapid development of the current national defense product capacity.