The Aksu River Basin landscape engineering, as a flagship project of the UN for ecological restoration, plays an important role in addressing climate change, protecting biodiversity, enhancing the value of ecological services and the quality of ecological products, and maintaining ecological security in the basin. Based on the law of regional differentiation, the principle of ecosystem coupling, and the mechanism of environmental effects, and based on the analysis of the coupling relationship between the spatiotemporal evolution of ecological vulnerability and ecological security, a ecological fragility evaluation index system for the Aksu River Basin"s mountains, rivers, forests, fields, lakes, grasslands, and sands system is constructed, consisting of 4 subsystems and 20 indicators. And apply the EFI method to analyze the contribution of various indicators and subsystems to EFI and their ecological effects.The larger the positive indicator value of EFI, the lower the ecological security.The larger the absolute value of the negative EFI indicator, the higher the ecological security. Obtained multi-source attribute data for various indicators in 1998 and 2023 through practical monitoring, experimental analysis, model simulation, remote sensing mapping, logical reasoning and empirical analysis, the weights and thresholds of each indicator are determined,which provide a data basis for ecological security evaluation through normalization and other methods. The results indicate that: (1) Ecological security is a complex and systematic issue. The interaction between various subsystems and their elements shows a certain degree of comprehensiveness, lag, complexity, and uncertainty in the ecological security of the basin. (2) The ecological security of the Aksu River Basin has been in a stable and improving state in recent 25 years. The EFI values are 0.08 and 0.06 in 1998 and 2023 respectively. According to the evaluation criteria, ecological fragility is further weakening and the degree of ecological security is continuously increasing. (3) The ecological security level of each subsystem and its contribution to the ecological security effect of the basin are different from each other. The indicators of the water resources subsystem are basically stable and gradually improving, and the fragility of the subsystem is becoming weaker while maintaining stability. The ecological security characteristics show an evolution pattern of becoming stronger while maintaining stability. The coexistence of positive and negative effects of relevant elements in the land resource subsystem, especially influenced by the variation of salinization index, has curbed the trend of improving ecological security. The EFI values of both biological resource subsystem and environmental subsystem are significantly decreasing, and the ecological security level is significantly enhanced. On the basis of revealing the evolution process and laws of ecological security, this paper proposes ecological security risk prevention and control, pattern optimization, process regulation, ecological restoration and management models, providing support for promoting green, low-carbon, and high-quality development of river basins.