The invention discloses a method and a system for modularized combined treatment of high-difficulty organic waste water, and the treatment system comprises: a primary settling tank, an adjusting tank, a reinforced flocculation tank, a precipitation separation tank, a secondary flocculation settling tank, a buffering water tank, a pH adjusting tank, a primary honeycomb microelectrolytic tank, a flocculation settling tank, a secondary honeycomb microelectrolytic tank, an intermediate tank, a heat exchanger, a microwave catalytic oxidation device, a secondary catalytic oxidation pot, and a re-oxidation filter pipe. The treatment method adopts a combined technical scheme of a multistage honeycomb iron carbon microelectrolytic module, a reinforced flocculation module and a microwave electro-catalytic oxidation module; the invention has the characteristics of high applicability, good treatment effect, and unit modularization; the modules can be combined and cascaded freely according to the waste water condition, and thus different waste water treatment effect requirements and waste water quantity requirements are adapted; the operation cost is low; the sludge amount is low; no secondary pollution is caused; and the method is an environment-friendly high-difficulty waste water treatment method.