Over the past four decades, many Chinese cities have faced serious ecological security pressures with rapid urbanization, especially, in the economically developed areas such as the Pearl River Delta urban agglomeration (PRD). The question of how to accurately evaluate the ecological security status and determine the influencing factors has become a realistic problem for the sustainable development of these cities. However, this analysis is hard to do because of the variable results derived from different evaluation methods and index systems. Robustness analysis is a broad method that is used for stable screening of different results. In this study, robustness analysis was conducted for 20 evaluation methods and 20 index systems. The most stable method was screened, which was the complex correlation coefficient method for indicator weight calculation, associated with the grey clustering method for ecological security evaluation. Moreover, the robustness analysis suggested that the stability of various index systems was better than that of various evaluation methods. According to the final urban ecological security pattern, the BP-DEMATEL model analyzed the influencing factors. The effect and intensity of each indicator were analyzed, which suggested that the total value of ecosystem service was the fundamental influencing indicator on the urban ecological security of the PRD. Six other driving influencing indicators including GDP per capita, normalize difference vegetation index, gross product of primary industry per unit area and anthropogenic disturbance index, as well as five characteristic influencing indicators were determined. Therefore, ecological elements were the most important guarantee of urban security in the PRD urban agglomeration. However, socio-economic elements played a key role in promoting urban ecological recovery. A creative approach was developed in this study to evaluate the ecological security of a region by integrating numerous methods and index systems. The comprehensive results provide constructive suggestions for the sustainable development of cities in the PRD urban agglomeration.