Stiffness modeling is an essential subject for the composition of robot control. Accurate stiffness modeling is helpful for improving the control accuracy of industrial robots, particularly under dynamic load circumstances. The classic virtual joint modeling (VJM) method is challenging in predicting the deformation of the end-effector throughout the full workspace due to the nonlinear deformation of the robot joint and its serial articulated structure. This paper proposes a full-space stiffness modeling method for robots based on the integration of a multi-layer perceptual (MLP) model and VJM. To provide enough training data for the MLP model, VJM is used to build a stiffness model with a small set of experimental data to generate 106,400 training data. A model-based transfer learning approach is proposed to improve the model’s accuracy and generalization regarding the difference between generated training data and actual experimental data. The VJM stiffness model is compared with the MLP stiffness model and the existing CNN-based transfer learning model based on the same experimental data. Considering the deformation prediction in the three directions in Cartesian space, the mean absolute error, standard deviation, and maximum error of the MLP model are decreased by at least 24.90%, 14.20%, and 8.50%, respectively, than the VJM. These prediction results demonstrate that the proposed modeling technique can significantly increase the accuracy of robot stiffness modeling, which is essential for position compensation in precise motion control of robots under dynamic load.