Organic Rankine Cycle (ORC) has been applied for generating power from different waste heat sources with higher thermodynamic efficiency. And the ORC's energy efficiency is closely dependent on the heat exchanger's operation. In this paper, a neuro-PID controller is proposed for the heat exchanger in ORC system for waste heat recovery. Compared with traditional control strategy, the proposed method could achieve better dynamics characteristic and have strong robustness against parameter and external disturbances. Finally, the simulation results illustrate the validity and superiority of the proposed approach.