The sustainable development of ecological environments is the basis of the sustainable development of inland river basins in arid areas with fragile ecological environments. The aim of our study is to diagnose the ecological problems of the Aksu River basin (ARB) and explore the ecological security pattern (ESP) and the layout and implementation path of ecological protection projects for mountains, rivers, forests, farmland, lakes, grasslands and deserts (MRFFLGD) in arid areas under different security levels. The Aksu River, the largest source of the Tarim River, was selected as the case study. The equivalent factor evaluation method (EFEM) was used to estimate the ecological service value (ESV), and the InVEST model was employed to quantify the ecological function indicators. By constructing the richness index, the ESV of the study area was measured spatially, and the ecological problems in the ARB were identified and diagnosed. Using cold/hot spot detection analysis and the minimum cumulative resistance (MCR) model, the ESPs at three security levels were constructed. The layout of ecological protection measures and the implementation path for MRFFLGD were studied. The results showed that the ESV of ARB showed an upwards trend from 1990 to 2018, and the three services of water conservation, waste treatment and soil formation and retention grew fastest. The value of ecosystem services in the study area in 2018 ranged from 5,390 yuan to 131,080 yuan/hm2. The high-value areas were mainly located in the oasis and the northern mountainous area, and the low-value areas were mainly located in the desert area. The ecological source areas of high, medium and low safety levels were 1806.3 km2, 3416.8 km2 and 4804.32 km2, respectively. Based on the spatial distribution of ESV in the ARB and the preliminary diagnosis of the basic ecological problems in the study area, three kinds of ecological protection engineering models, namely, conservation, natural restoration and assisted regeneration, were proposed for the four types of ecological protection zones. To provide a decision-making basis for ecological environmental management and regional sustainable development in the ARB, the optimization patterns of points (6 key ecological protection projects), lines (ecological corridors) and polygons (ecological source areas) were constructed. The results of this study can also serve as a reference for ecological environmental protection in other arid inland river basins.