The invention provides a docking type multi-module cooperative flexible cone-rod docking mechanism and a working method thereof, the docking mechanism includes a plurality of active ends mounted on the active aircraft and a plurality of passive ends mounted on the docked aircraft, the active end and the passive end correspond one by one, An active end and a passive end form a set of modules, Active and docked aircraft complete initial capture with the aid of a manipulator, the passive end is tapered, The active end includes a housing assembly, a drive assembly, a drive assembly, and a capturerelease assembly. The housing assembly supports and connects the drive assembly, the drive assembly, and the capture release assembly. The drive assembly drives the drive assembly and the capture release assembly to reciprocate linearly along the housing assembly, and the capture release assembly is used to lock or release the passive end. The invention has the advantages of small volume, simple system and modular design, avoids the influence of the conventional collision-type docking mechanism on the system stability by using the flexible docking technology, and improves the docking reliability and safety.