In this paper, in-situ nanomechanical measurement and ex-situ morphology study were conducted to investigate the surface roughness effects of current collectors on the performance of thin film silicon anodes. The in-situ analysis quantifies electrochemical processes and associated mechanical stress such as silicon-lithium alloy formation during charge and discharge. Upon lithiation, after SEI formation (approximately below 0.35 V), both alpha-Si films deposited on the pristine and FeCl3-etched copper experience elastic deformation with a rapid rise of a compressive stress. The films begin to deform plastically after the stress reaches compressive yield strength. Upon delithiation, the alpha-Si on the pristine copper has shown to have stress dissipation at a tensile stress of 0.28 GPa. However, the tensile stress of the a-Si on the FeCl3-etched copper continues until the stress reaches 0.4 GPa at the end of delithiation. In addition, the silicon anode was found to form small islands on roughened current collector (instead of peel-off from fiat current collector), indicating the design of the current collector may play an important role in the performance of lithium ion battery.