Cost overrun during construction is one of the most common problems occur in construction projects around the world, which also includes the area of Chongqing in China. At present, there are few studies related to cost overruns at the construction stage of high-rise residential building projects (HRBPs) in Chongqing. The purpose of this study is to develop effective control measures from the contractor’s perspective to help projects to minimize cost overruns during the construction phase of HRBPs in Chongqing. Firstly, through the literature review and semi-structured interviews, 65 cost overrun-related risk factors in construction projects were identified. All the risk factors have been prioritized through the analytic hierarchy process (AHP) based on their importance to project success. Out of the 65 factors identified, 12 were classified as the critical ones that have a great potential to instigate a cost overrun during construction to take place in the real project. There were four risk factors that have the greatest impact on cost overruns, and their weights were 0.04 or above, including low bid, force majeure, undetailed/inaccurate geological survey data, and increased loan interest rates. Finally, control measures were developed for these four critical cost overrun risk factors (CCORFs). The measures developed provided a guideline to control the risk of cost overruns and clear control key points to help contractors minimize cost overruns on construction projects.