The invention relates to a treatment method of structural conflict in an AOP application program based on metadata and a reflection mechanism, which comprises the following steps: 1) taking a meta-layer in the structure of a reflection system as a middle layer between a basic program and an Aspect; 2) creating an XML file used for describing logic information, physical information and mapping relation between the two which correspond to the basic program in a conceptual layer for a type or the method which needs to be reflected in the basic program; 3) adding or updating a label for the basic program; 4) updating the physical information which corresponds to the logic information according to the logic information in the XML file; and 5) automatically generating a meta-layer program by a conversion program and completing the realization of refining and reflection in the structure of the reflection system by the metal-layer program. The treatment method has the benefits of being capable of flexibly selecting the size of reflection particle size, leading the implementation way of the program to be more flexible, having no limit requirements of AOP language and leading the using method to have stronger universality.