According to the two-stage electrochemical cross-linking electrodialysis desalination treatment system and the application thereof, high-salinity wastewater is treated based on the treatment system, the problem that in the prior art, membrane pollution is easily caused by organic matter pollution in wastewater can be effectively solved, meanwhile, synchronous acid-base separation is achieved, the effluent quality is improved, and the treatment cost is reduced. The water treatment process steps are reduced. The system comprises at least one two-section electrochemical cross-linking electrodialysis desalination treatment unit, the two-section electrochemical cross-linking electrodialysis desalination treatment unit comprises an outer anode and an outer cathode which are oppositely arranged, and the outer anode and the outer cathode are arranged in an area between the outer anode and the outer cathode. A first bipolar membrane, a cation exchange membrane, an inner cathode, an inner anode, an anion exchange membrane and a second bipolar membrane are sequentially arranged in the direction from the outer anode to the outer cathode; and the inner side cathode and the inner side anode are respectively a mesh-shaped cathode and a mesh-shaped anode.