The invention discloses an electrochemical microorganism autotrophic nitrogen removal sewage treatment method and system. The system comprises a microorganism electrolytic tank shell, a sealed cover, a microorganism positive electrode, a microorganism negative electrode and a power supply, wherein the sealed cover covers the microorganism electrolytic tank shell to form a closed space; the microorganism positive electrode and the microorganism negative electrode are connected with a negative electrode and a positive electrode of the power supply respectively, a short-distance nitrification microorganisms are enriched on the microorganism positive electrode, and denitrification methane anaerobic oxidation microorganisms are enriched on the microorganism negative electrode; the side, close to the microorganism positive electrode, of the microorganism electrolytic tank shell is provided with a water inlet, and the side, close to the microorganism negative electrode, of the microorganism electrolytic tank shell is provided with a water outlet. An inorganic carbon source put-in opening is formed in the position, close to the microorganism negative electrode, between the microorganism positive electrode and the microorganism negative electrode. By means of one electrolytic tank, short-distance nitrification, electrochemical methane production and methane anaerobic oxidation are effectively coupled, reaction mass transfer efficiency is accelerated, occupied area is small, and capital construction investment is small.