With the rapid economic development in China, water shortage and water quality deterioration in rivers have become serious problems for ecological systems. Recognition of such situation of rivers has led to the establishment of the science of instream flow assessment. Instream flow assessment can determine the quantity and quality of water required for ecosystem conservation and resource protection.The majority methods of instream flow assessment can be grouped into four categories, such as hydrological, hydraulic rating, habitat simulation (or rating), and holistic methodologies. Hydrological method is the most widely used and suitable for China, with lack of detailed ecological data. The hydrological method has been criticized for offering an assessment resolution only from low to moderate, and encompassing limited temporal differences in flow allocations. In order to increase assessment resolution a dynamic method to determine the instream flow for a wide range of ecological states was developed with the combination of monthly percentile curve method and hydrological index. Monthly percentile curve is widely used in instream flow assessment in China while lacking linkage with ecosystems. Hydrological index is closely relevant with ecosystem while it can’t be directly used in instream flow assessment. Based on a screening of the most popular hydrological indices, an amended hydrological index method, AAPFD, was used to assess the instream flow of the range of scenarios. AAPFD can be used as an indicator of hydrological alteration. We combined monthly percentile curve and hydrological index to develop a dynamic method. Monthly percentile curve was employed to make out a range of scenarios, and development status of actual water resources was used to adjust the range of scenarios. Then AAPFD was used to evaluate every scenario, and each scenario was linked with AAPFD. The number of AAPFD was relevant to ecosystems, and then each scenario was linked with ecosystems. Nianchu River is a main branch of Yarlung Zangbo River, the largest river in Tibet and the highest river in the world. The dynamic hydrological method developed in this paper was then used in Nianchu River and nine scenarios were set to assist water resources management. Scenario 1 indicates a state that hydrological regime is seriously altered, and scenario 9 indicates a state that hydrological regime is close to natural state. According to the water resources situation and social development status the department of water resources should take scenario 3 and scenario 4 as the management target in the near future, and the corresponding AAPFD is 3.07 and 2.59. These scenarios indicate states moderately altered by water resources development.