The Magnetic Screw Motor (MSM) has emerged as a promising technology for precision linear drives, offering non-contact operation, high efficiency, and low maintenance. However, MSMs face challenges in maintaining performance stability due to transmission ratio fluctuations caused by structural flexibility. Traditional control strategies, such as deadbeat direct torque and flux control (DB-DTFC), offer fast and precise torque and flux tracking, making them effective in many motor control applications. However, in MSMs, these strategies are limited by their inability to effectively reject disturbances arising from the variable transmission ratio. To address this limitation, we propose a hybrid control strategy integrating Active Disturbance Rejection Control (ADRC) with Deadbeat Direct Torque and Flux Control (DB-DTFC). Furthermore, a Dynamic Flux Compensation (DFC) strategy is incorporated for hierarchical flux adaptation. By leveraging ADRC’s disturbance estimation and compensation capabilities alongside DFC, the proposed method significantly improves disturbance rejection and system robustness. Simulation results validate the effectiveness of the proposed approach in enhancing MSM performance under varying operational conditions.