Objective To compare the set-up errors of two body membrane usage methods so as to provide a better set-up method for precision radiotherapy. Methods Fifty patients with lung cancers who had been treated in Department of Radiation Oncology in the hospital from August 2013 to October 2014 were selected and randomly divided into Conventional Body Membrane Group and Window Body Membrane Group. All the patients received intensity-modulated radiation therapy (IMRT). Each patient carried on cone beam computerized tomography (CBCT) once a week to measure set-up errors online and correct set-up errors timely. Statistical analysis of the set-up error data of the two groups was performed. Results Set-up errors in the left-right, head-foot, anterior-posterior direction were (2.62±2.06) mm and (2.00±1.61) mm (P=0.008), (3.78±2.86) mm and (3.10±1.86) mm (P=0.027), (1.67±1.32) mm and (1.42±1.10) mm (P=0.97) in Conventional Body Membrane Group and Window Body Membrane Group, respectively. Conclusion The usage of window body membrane could reduce set-up errors effectively in the left-right and head-foot direction and improve the set-up accuracy.