[Objective] To understand the risk of water quality safety in main canal for water diversion from Yellow River to Qingdao City, in order to provide basis for the safety management of main canal, and to ensure the the drinking water safety of Qingdao City.[Methods] Based on the monitoring data obtained along the main canal, the key control factors which determine the water quality in the main canal were identified, and a list of the water quality safety risks was determined by further analysis of the risk factors.[Results] The water quality of the main canal was improved firstly, and then deteriorated. Nutrients were the main indexes affecting the water quality of the main canal. The south-to-north water diversion project alleviated the eutrophication of the main canal obviously. There were larger sources of iron and phosphorus pollution in the main trunk canal between Songzhuang water diversion and water inlet of Jihongtian reservoir.[Conclusion] It is feasible to apply the key control factors identification method in the long distance water diversion projects. The existing safety risks in the main canal include total nitrogen and total phosphorus from the Yellow River, organic matter and sulphate from the south-to-north water diversion project, and iron, phosphorus and organic pollutants in the latter half of the main canal. The potential safety risks are eutrophication and release of metal ions caused by the changes of water intake volume in south-to-north diversion or the Yellow River and the failure of the wetland system.