The invention discloses a flexible automatic loading system and application thereof. The flexible automatic loading system aims to solve the problems that an existing bagged material loading device lacks a corresponding automatic scanning and positioning system and is low in automatic degree. According to the flexible automatic loading system and the application thereof, mechanisms of the loadingsystem are subjected to completely-new optimization design, a carriage is subjected to automatic scanning positioning through a laser scanning positioning unit, a material is conveyed through a feeding unit, and through a stacking and loading unit, the material is effectively placed on a designated position of the carriage to achieve material automatic loading. The flexible automatic loading system can meet the demands of the sizes and height change of various material conveying vehicles, the loading path can be automatically planned according to the size information and loading tasks of a target vehicle carriage, automatic loading is achieved according to data provided by the laser scanning positioning unit, and in the whole loading process, only loading task manual issuing is needed. According to the flexible automatic loading system, the labor intensity of workers can be effectively reduced, the bad loading environment is avoided, the production efficiency of enterprises is improved, the labor cost of the enterprises is reduced, and the high application value is achieved.