It is essential for human-robot interaction to accurate joint torque value estimation of industrial robots without force/torque (F/T) sensors. The most common method to estimate the value of robot joint torque is based on dynamic model parameter identification. However, no matter how elaborate the modeling methods are used, there are always uncertainty errors when robot’s joint rotation direction changes. In this paper, an identification framework is proposed to estimate optimal model parameters, and a deep learning network is proposed to compensate for the uncertainty errors caused by the unmodeled dynamics part. At first, the dynamic parameters are estimated during the Least Squares (LS) identification process considering the noise influence and data outliers, and the nonlinear friction model is unified into the identification framework. Secondly, based on Long-Short Term Memory (LSTM) network, an error compensation model (ECM) is proposed to establish the mapping relationship between the joint motion and the identification errors. Finally, a 6-DOF robot is used for parameter identification and ECM validation. Experimental results show that the proposed identification method is better than the LS method. Compared with the torque value estimated by the identification method, the proposed ECM can compensate for the uncertainty errors and improve the torque estimation accuracy.