The invention provides a TSV (through silicon via)-interconnect-based system in package electromagnetic coupling suppression method. Grid ground structures and P+ contact arrays are arranged to form electromagnetic shielding planes, the virtual electromagnetic shielding planes are connected to finally form a three-dimensional global electromagnetic shielding structure by adopting grounded TSV arrays, transverse electromagnetic coupling of the same layer of substrate is suppressed through distributed electromagnetic shielding units and the grounded TSV arrays, and electromagnetic coupling in the perpendicular direction is shielded through the virtual electromagnetic shielding planes, so that electromagnetic coupling of the substrates in the horizontal direction and the perpendicular direction is simultaneously isolated. According to the method, a low-impedance local loop is designed for an interference noise source, and noise current is guided to form a loop in a local area, so that the aim of preventing noise to be coupled to other places is fulfilled, and the problems of poor three-dimensional transmission noise suppression capability, shielding bandwidth and shielding performance of a current electromagnetic shielding technology are solved.