The invention provides a comprehensive diagnosis method and a diagnosis system thereof for diagnosing the defects of a substation grounding grid. The diagnosis method establishes the topology model of the substation grounding grid and the software arithmetic of the grounding diagnosis system which takes a node voltage optimization model as a core; corresponding current excitation nodes and potential reference nodes are found out in the substation grounding grid and voltage measurement sensors are arranged at all nodes; after excitation signals are applied to the current excitation nodes, the sensors obtain the detection signals and transmit the detection signals to the comprehensive diagnosis system which is used for diagnosing the defects of the substation grounding grid and connected with the sensors; the software arithmetic of the comprehensive diagnosis system for diagnosing the defects of the substation grounding grid is used for calculating relevant parameters of the grounding grid branch resistance, thus determining the positions of the failure defects of the substation grounding grid; the diagnosis system consists of a power supply device, a filter device, a data collecting device and a background PC machine and has the advantages of reasonable design proposal, convenient operation, exactly detecting the defects of the main net of the grounding grid and the grounding down lead wire without excavating the ground surface, and the like.