To clarify the effectiveness of the unified management of the Tarim River, the impacts of human activities on water resources and runoff in the source area and mainstream were analyzed based on the runoff and water consumption data of source area and main stream. The methods of nonparametric tests, periodic superposition model, anomaly and coefficient of variation were used. The results showed that: 1) The impact of human activities on water in source area decreased after the implementation of integrated management (2001) and unified management measures (2010). Compared with climate change, the influence of human activities on the water source in source area became weaker, and the phenomenon of excessive water diversion in the river basin has been improved. 2) After the implementation of unified management, the difference of the coefficient of variation of anomaly percentage of the runoff in the headstream and mainstream reduced from 6.63 to 0.24. The average value of anomaly percentage difference changed from -19.6% to -4.9%. The curve of cumulative anomaly of runoff difference between headstream and mainstream rose at first and then fell down. The fluctuation of runoff in the headstream and mainstream decreased, especially the mainstream, and the coordination of runoff became stronger. The results indicated that after the implementation of the unified management, man-made diversion has been effectively controlled; the ability of managing and controlling the runoff of the river has been significantly improved; and unified management has achieved remarkable results.