In order to effectively design the viscous dampers in the isolation layer of base-isolated structures, an optimal design method was proposed to determine the damper parameters with the design emphasis of displacement and shear force of isolation layer. The seismic energy balance equation of base-isolated structures with viscous dampers was established. A simple method was given for predicting the maximum displacement and total shear coefficient of isolation layer using input energy at the end of earthquake. The accuracy of the prediction method was verified by dynamic time history analysis. Results show that the prediction accuracy increased with the increase in the additional damping ratio. The response reduction effect of the isolation layer under the optimal shear design was analyzed. Based on the design principle of solving the minimum value of the combination function of response ratios, an objective function for the optimal design was constructed by using the linear combination of total shear response ratio and displacement response ratio. The responses of the isolation layer under four typical design objectives were analyzed, and the optimal design process of the isolation layer with viscous dampers was given. Finally, a six-story steel frame base-isolated structure with viscous dampers was designed and its seismic performance was verified. The design example proved that the optimal design method is of feasibility and convenience. The prediction method can be used as a response checking method with good accuracy and safety. The viscous dampers design method which can optimize the displacement and shear response of isolation layer is efficient, and the design process is suitable for manual calculation.