This paper proposes real-time control strategies that can be applied in a full-scale advanced phase isolation ditch (APID) process. Real-time operation mode control (OMC) and aeration section control (ASC) strategies were developed to cope more stably with fluctuations in the influent loading and to increase the nitrification and denitrification reactions within the entire volume. The real-time OMC and ASC strategies were evaluated using mathematical models. When the NH4-N in the reactor was maintained at a high level, appropriate control actions, such as continuing the aeration state, stopping the influent inflow and increasing the aeration section, were applied in the APID process. In contrast, when the NOX-N in the reactor was maintained at a high level, the non-aeration state, influent inflow, and decreased aeration section were continued. It was concluded that stable operation in the APID process could be achieved by applying real-time OMC and ASC strategies developed in this study.