In the context of urban expansion and climate change, the world is under pressure from multiple ecological risks. Key ecological protection areas play a pivotal role in preserving ecological stability and promoting development. Due to its unique geographical conditions, the Yellow River basin has been facing huge ecological risk pressure. In the affected area of the Lower Yellow River (AALYR) as an agricultural hub, ecological protection has gradually become a key factor restricting the development of cities and agriculture. Taking AALYR as an example, the landscape ecological risk assessment (LERA) system is established based on three aspects “natural environment—human society—landscape pattern”. We construct a comprehensive cumulative resistance surface based on the risk assessment results as the basis for the future study. Ecological corridors are identified by minimum cumulative resistance (MCR) models to establish and optimize Ecological security pattern (ESP) in the AALYR. We found that the landscape ecological risks (LER) in the study area show a uniform spatial distribution, with a slightly higher distribution in the northeast than the southwest. The ecological risk levels are generally high in AALYR, indicating a more severe risk problem in this area. A total of 56 ecological sources were identified, with a total area of 21176 km2. The ecological sensitivity of AALYR was high, and 99 ecological corridors and 59 ecological nodes were extracted. Ecological corridors and nodes were consistently and densely distributed throughout the study area. The network analysis method improves the stability of the network structure after optimization. Based on the key components of the ESP, with the combination of geographical characteristics and local policy planning guidance, we constructed the “One Belt and One Axis, Two Cores and Two Corridors, Four zones” ESP. The study results may offer guidance and suggestions for the construction of ESP and ecological environment protection system in the world’s major river basins, and may also provide information for ecological planning of other similar river basins in the world.