The invention relates to an integrated sub-three-phase separated-type internal electrolysis reactor and applications. The integrated sub-three-phase separated-type internal electrolysis reactor is composed of four control systems including a water intake and back water flushing control system, an aeration and back air flushing control system, a PLC (programmable logic controller) automatic control system, a reflux and pollution discharge control system; the reactor can be divided into four functional areas including a buffer water distribution area, a bearing area, a material filling area, a back wash expansion area, a sub-three-phase separation area and a water discharge area. The integrated sub-three-phase separated-type internal electrolysis reactor and an operation method provided by the invention not only overcome the phenomena of hardening and passivation of the internal electrolysis material, but also can estimate the advantages and disadvantages of the quality of the internal electrolysis material and the service life of the filling material, thus providing convenience for the wide popularization and high-difficulty industrial waste water treatment of the internal electrolysis technique.