In the past four decades, China has achieved tremendous economic success, but it has also faced serious ecological security (ES) problems. The land use/cover change (LUCC) plays a decisive role in the issue of ES. LUCC and ES evaluation were combined by predicting the change in land use and simulating ES pattern. Taking the Pearl River Delta urban agglomeration (PRD) as the study area, the temporal changes of land use were predicted by the CA-Markov model, and the land use pattern in three different scenarios in 2025 was simulated. Based on the Pressure-State-Response (PSR) model, the ES evaluation of the PRD in 2005, 2010 and 2015 was carried out, and the safety level dropped from 75.39% to 66.67% in this period. Spatial autocorrelation analysis was performed by the GeoDA to reflect the dynamic of ES pattern of the PRD, which suggested that there is greater heterogeneity within the PRD, and the homogenous sub-region continues to increase. Through change the transition probability among different land use types, three scenarios were set: Inertial development, Over expansion, and Ecological protection scenario, which showed that the expansion of construction land (accounting for 18.58%, 20.12% and 17.93% respectively) must occupy agricultural and forest lands and lead to decrease on ES level, the safety level are accounting for 79.07%, 78.30% and 79.95% in the three scenarios respectively. The ES pattern of the PRD was described, the central sub-region of the PRD with high urbanization have relative low ES, and the periphery sub-regions with good ecological order have high ES level, there are more than 63.59% and less than 4.06% of unsafety level of Dongguan and Zhaoqing respectively, which are both the representative city of these two sub-regions. Based on the spatial-temporal dynamic of urban ES, the optimized ES pattern of the PRD was proposed, three eco-functional zones were determined: ecological conservation zone, living environment guarantee zone and ecological restoration zone. The eco-functional zones have defined the leading ecological functions of each sub-region and could gradually improve the integrity and connectivity of the entire ecosystem of the PRD, which provides valuable knowledge for understanding and planning regional city management.