Background: Patients with symptomatic internal carotid artery (ICA) or middle cerebral artery (MCA) occlusion with haemodynamic insufficiency are at high risk for recurrent stroke when treated medically. Methods: The Carotid or Middle cerebral artery Occlusion Surgery Study (CMOSS) trial is an ongoing, government funded, prospective, multicentre, randomised controlled trial. The CMOSS will recruit 330 patients with symptomatic ICA or MCA occlusion (parallel design, 1: 1 allocation ratio) and haemodynamic insufficiency. Participants will be allocated to best medical treatment alone or best medicine plus extracranial-intracranial (EC-IC) bypass surgery. The primary outcome events are all strokes or deaths occurring between randomisation and 30 days post operation or post randomisation and ipsilateral ischaemic stroke within 2 years. Recruitment will be finished by December 2016. All the patients will be followed for at least 2 years. The trial is scheduled to complete in 2019. Discussion: The CMOSS will test the hypothesis that EC-IC bypass surgery plus best medical therapy reduces subsequent ipsilateral ischaemic stroke in patients with symptomatic ICA or MCA occlusion and haemodynamic cerebral ischaemia. This manuscript outlines the rationale and the design of the study. CMOSS will allow for more critical reappraisal of the EC-IC bypass for selected patients in China.