The invention discloses an electromagnetic characteristic analysis method and system for an electrically large-size target with a complex structure, and the method comprises the steps: carrying out the surface triangulation of the target, setting a regional decomposition seed, completing the regional autonomous decomposition of the target based on the decomposition seed, obtaining a plurality of decomposition parts, and numbering the decomposition parts; creating a plurality of parallel threads, specifying a main thread and sub-threads, and distributing the number and serial number of decomposition parts responsible for each sub-thread; for each sub-thread, constructing a comprehensive function for all responsible decomposition parts, compressing the self / mutual impedance matrix and the excitation matrix of the decomposition parts by utilizing the comprehensive function, and reporting a result to a main thread; the main thread detects connection boundaries between different decomposition components, and calculates a self / mutual impedance matrix and an excitation matrix of the connection boundaries; and constructing a target overall compression matrix equation, solving the equation,and combining with the comprehensive function definition to obtain the electromagnetic characteristics of the target in space. The method solves the problems of low processing efficiency and the likein the prior art, and greatly improves the comprehensive processing efficiency of the SBFM.