The invention relates to an aeronautical data chain information-based civil aircraft aviation electronic verification system and a method thereof. The civil aircraft aviation electronic verification system comprises an aeronautical data chain information receiver, a data chain decoding module, a configuration management module, a database module, a verification platform tool module, a task module, a contrastive analysis application module and an analysis terminal, wherein the database module is used for storing machine type data and performance data of an airplane, local civil airline data and actual flight data; the task module is used for calling the data in the database module according to tasks and acquiring actual track path data which is needed by contrastive analysis verification and is generated based on the aeronautical data chain information; and the contrastive analysis application module is used for comparing the data of a verified object acquired by the verification platform tool module with the actual flight data of the task module, and providing a digital difference value report or a track goodness of fit report according to a comparison point set by a user. The civil aircraft aviation electronic verification system and the method thereof support a digital development environment through the current civil aviation communication data chain technique so as to provide a vivid testing or verifying means for an avionics system.