The effect of soil-structure interaction (SSI) cannot be neglected in semi-active vibration control of structures located on soft soil. To investigate the mitigating effect of magnetorheological (MR) damper on the semi-active control of structures considering the SSI, shaking table tests were conducted to evaluate the performance of the MR damper-based semi-active control system for structures on soft soil. In addition to a novel fuzzy control method based on online learning deep neural network (OL-DFNN), various control strategies, including passive OFF, passive ON, ON–OFF and deep neural network fuzzy control (DFNN) were systematically evaluated. The test results showed that the OL-DFNN control method exhibited superior adaptability to varying ground motion and structural dynamic characteristics compared to the other control methods. In particular, the OL-DFNN controller effectively mitigated the peak displacement and root mean square displacement, outperforming the passive OFF, passive ON, ON–OFF and DFNN control strategies. The test results highlight the effectiveness of the OL-DFNN control method in addressing the challenges posed by dynamic and time-varying characteristics in structural vibration control systems considering SSI.