The coping strategy of a CANON (completely autotrophic nitrogen removal over nitrite) reactor working at room temperature was investigated using response surface methodology. The total nitrogen (TN) removal efficiency was taken as a dependent variable. The temperature (X), dissolved oxygen (DO) concentration (Y), and influent nitrogen loading rate (Z) were taken as independent variables. Results showed that the relation of these three independent variables can be described by the TN removal efficiency expressed as −5.03 + 1.51X + 45.16Y + 30.13Z + 0.26XY + 1.84XZ − 0.04X2 − 9.06Y2 − 99.00Z2. The analysis of variance proved that the equation is applicable. The response surface demonstrated that the temperature significantly interacts with the DO concentration and influent N loading rate. A coping strategy for the CANON reactor working at room temperature is thus proposed: altering the DO concentration and the N loading rate to counterbalance the impact of low temperature. The verification test proved the strategy is viable. The TN removal efficiency was 91.3% when the reactor was operated under a temperature of 35.0 °C, a DO of 3.0 mg/L, and a N loading rate of 0.70 kgN/(m³ d). When the temperature dropped from 35.0 to 19.2 °C, the TN removal efficiency was kept at 88.7% by regulating the influent N loading rate from 0.7 kgN/(m³ d) to 0.35 kgN/(m³ d) and the DO concentration from 3.0 to 2.6 mg/L.