In the power system of a polysilicon reduction furnace, especially during the silicon rod growth process, the issue of insufficient temperature control accuracy arises due to the system’s nonlinear and time-varying characteristics. To address this challenge, a dual-loop control system is proposed, combining model-free adaptive control (MFAC) with an improved PID controller. The inner loop utilizes a hysteresis PID controller for dynamic current regulation, ensuring fast and accurate current adjustments. Meanwhile, the outer loop employs a hybrid MFAC-based improved PID algorithm to optimize the temperature tracking performance, achieving precise temperature control even in the presence of system uncertainties. The MFAC component is adaptive and does not require a system model, while the improved PID enhances stability and reduces the response time. Simulation results demonstrate that this hybrid control strategy significantly improves the system’s performance, achieving faster response times, smaller steady-state errors, and notable improvements in the uniformity of polysilicon deposition, which is critical for high-quality silicon rod growth. The proposed system enhances both efficiency and accuracy in industrial applications. Furthermore, applying the dual-loop model to actual industrial products further validated its effectiveness. The experimental results show that the dual-loop model closely approximates the polysilicon production model, confirming that dual-loop control can allow the system to rapidly and accurately reach the set values.