The inverse dynamics model of an industrial robot can predict and control the robot’s motion and torque output, improving its motion accuracy, efficiency, and adaptability. However, the existing inverse rigid body dynamics models still have some unmodelled residuals, and their calculation results differ significantly from the actual industrial robot conditions. The bootstrap aggregating (bagging) algorithm is combined with a long short-term memory network, the linear layer is introduced as the network optimization layer, and a compensation method of hybrid inverse dynamics model for robots based on the BLL residual prediction algorithm is proposed to meet the above needs. The BLL residual prediction algorithm framework is presented. Based on the rigid body inverse dynamics of the Newton–Euler method, the BLL residual prediction network is used to perform error compensation on the inverse dynamics model of the Franka robot. The experimental results show that the hybrid inverse dynamics model based on the BLL residual prediction algorithm can reduce the average residuals of the robot joint torque from 0.5651 N·m to 0.1096 N·m, which improves the accuracy of the inverse dynamics model compared with those of the rigid body inverse dynamics model. This study lays the foundation for performing more accurate operation tasks using industrial robots.