The impacts of climate change on hydrological processes in Tibetan Plateau are complicated and sensitive, and the resulting water resource change could have profound influences. Nujiang River, sourcing from Tibetan Plateau, is an important international river in southwest China. Taking use of long term records, air temperature and precipitation variations in the middle and upper Nujiang River Basin during 1960 to 2009 were analysed. On the other hand, seasonal flow, extreme flow, and flow duration curve in Daojieba station were compared to study the variation characteristics of low flow and their responses to climate change in recent 50 years. The results show that winter and spring air temperature had increased, and the rate in winter was higher than that in spring, which increased with altitude. In Naqu station in the river source, the increasing rate of winter temperature could reach 0.81℃/10 a. In addition, daily minimum air temperature in winter and spring in the middle and upper Nujiang River Basin had increased more quickly and significantly than daily maximal air temperature, which showed that increasing mean temperature was largely due to rising nocturnal temperature. The trends of winter and spring precipitation were both increasing. The increasing rate of spring precipitation in Naqu, Suoxian, and Dingqing stations were between 6.5 and 7.7 mm/10 a, and spring precipitation in these 3 stations in 2000 s were 54.4%, 35.6%, and 18.0% more than the average value. Winter and spring flows in Daojieba station had increased significantly, and the increasing rate were 18 and 44 (m~3/s)/10 a, respectively. Winter flows in 1990s and 2000s were 7.3% and 10.7% higher than the average value, while the anomaly of spring flow in 1990s reached 16.8%. On the other hand, whether annual minimum of 1-day, 7-day, 30-day, and 90-day moving average flows, or Q75, Q90, and Q95, the value in 1990s and 2000s were all much higher than those in other decades, which showed that low flow had increased from 1990s. For instance, between 1960 and 2009, there were 10 years with minimum daily flow greater than 400 m~3/s, which were all in 1990s and 2000s. While 20 years with minimum daily flow less than 350 m~3/s, among which only 2 years were in 1990s and 2000s. In addition, Q75 in Daojieba station in 1960s, 1970s, and 1980s were 489, 510, and 488 m~3/ s respectively. While in 1990s and 2000s, the values were 577 and 563 m~3/s, which were 10%-18% higher than previous 3 decades. The increase of low flow in the middle and upper Nujiang River Basin could be attributed to the increasing air temperature and precipitation in winter and spring. At first, increasing precipitation would generate more flow. Secondly, rising air temperature may accelerate melting processes of snow and ice. In addition, frozen soil degradation caused by climate warming could also affect hydrological processes.