Methods of solving some of the critical design consideration associated with the thermocline storage system with unusual physical boundary conditions bring new problems: the effect of insert liner should not be ignored with small solid filler size, and it is hard to take advantage of truncated cone shaped tank for decreasing the potential of thermal ratcheting and increasing the maximum height of the tank, both while maintaining a good efficiency. In this study, a transient two-dimensional and two-temperature model is developed to investigate the heat transfer and fluid dynamics in a molten salt thermocline thermal storage system. After model validation, the effects of physical boundary conditions including insert liner and sloped wall on the thermal performance of thermocline storage system is investigated through the entropy generation analysis. The results show that both of the axial and radial convex size of the liner should be as small as possible, resulting in smaller average velocity and less disturbance in the flow. The truncated cone shaped tank has an advantage in the charging process with low entropy generation in molten salt and solid material, while it goes against the discharging process. It is found that larger inclined angle of the sloped wall causes smaller thermocline thickness and entropy generation with the same tank height and tank volume for truncated cone shaped tanks. Besides, larger tank height is better for the truncated cone shaped tanks with the same tank volume. (C) 2016 Elsevier Ltd. All rights reserved.