For the operation of the supercritical once-through boiler generation units, the control of the temperature at intermediate point (IPT) is highly significant. IPT is the steam temperature at the outlet of the separator. Currently, PID control algorithms are widely adopted for the IPT control. However, PID cannot achieve the optimal performances as the units’ dynamic characteristic changes at different working points due to the severe nonlinearity. To address the problem, a new control algorithm using affine nonlinear system is adopted for a 600 MW unit in this paper. In order to establish the model of IPT via affine nonlinear system, the simplified mechanism equations on the evaporation zone and steam separator of the unit are established. Then, the feedback linearizing control law can be obtained. Full range simulations with the load varying from 100% to 30% are conducted. To verify the effectiveness of the proposed control algorithm, the performance of the new method is compared with the results of the PID control. The feed-water flow disturbances are considered in simulations of both of the two control methods. The comparison shows the new method has a better performance with a quicker response time and a smaller overshoot, which demonstrates the potential improvement for the supercritical once-through boiler generation unit control.