The ecological network (EN) is crucial for sustainable development of arid regions worldwide. Traditional EN analysis methods have primarily neglected the impact of geographical heterogeneity, impeding effective management of arid regions' fragile ecosystems. With China's largest arid region, the Tarim River Basin (TRB), as an example, we established a framework incorporating geographical heterogeneity into EN analysis and evaluated its influences to network performance and robustness. The results indicated that 1) the EN comprises 176 mountain sources, 60 oasis sources, and 24 desert sources connected by 736 ecological corridors, corresponding to the TRB's mountain-oasis-desert (MOD) geomorphological structure. 2) Mountain sources have high centrality, connectivity, and vulnerability, contributing 67.6 %, 68.5 %, and 61.7 % to the average degree, average clustering coefficient, and average path length. Oasis sources have higher centrality and average degrees than mountain sources. The corridors between oasis sources account for 27.5 % of the average path length, serving as important ecological pathways. 3) Mountain sources contribute the most to EN stability under both deliberate and random attacks, followed by oasis sources. This study highlights the role of mountain sources in sustaining ENs and oasis sources in connecting components, offering insights for targeted conservation and restoration in the TRB and similar arid regions.