Recently, most semi-arid basins in China have experienced vegetation greening under significant water and thermal conditions changes, which has exacerbated the shortage of water resources despite the positive effect of increasing carbon sinks and reducing carbon emissions. The study of vegetation response under variations of water and thermal conditions can help to understand the mechanism of the balance between the hydrological processes and vegetation pattern and is of great significance for the sustainable utilization of water resources and ecological protection. However, few studies have focused on the time-periodic and segmented response mechanisms of vegetation dynamics to variations of water and thermal conditions, resulting in unclear mechanisms of trade-off between vegetation greening and water resources. This study analyzed the varied trends of water and thermal conditions and discussed the spatio-temporal response of vegetation from two points: overall trends and varied processes at the upper and middle Hailar River Basin from 1980 to 2012 by using trends and wavelet period analysis. The results show that: (1) spatially, the average annual precipitation increased and the temperature decreased from west (grassland) to east (forest). Compared with the grassland area, the runoff and the Normalized Difference Vegetation Index (NDVI) in the forest area showed larger, and indicated slower warming and larger precipitation declining. (2) Temporally, the average annual precipitation and the runoff slightly decreased with a trend of 10 mm/10 a and 19.3 mm/10 a, respectively; the average annual temperature and NDVI in the growing season increased significantly with a trend of 0.65 ℃/10 a and 0.003-0.006/10 a, respectively. The results suggested that warming and drying inhibited the runoff and increased the vegetation growth, even in the context of precipitation increased and smooth increasing trend of temperature after 1998, showing the accumulative effect of water and thermal. (3) The periodicity of precipitation, temperature, runoff and NDVI were 6.9, 6.9, 13.8 and 9.8 years, respectively. The overall vegetation change trend was mainly dominated by temperature, and vegetation greening was an important factor for runoff decreasing on the overall trend of vegetation; runoff dynamics and periodic patterns were mainly controlled by precipitation, while that of vegetation was influenced by the combination of precipitation and temperature, and the response process was affected by the cumulative effects of water and thermal periodic trend conditions. The study strengthens the understanding of the trade-off between water resources and vegetation greening and provides a reference basis for vegetation management and water resource utilization at semi-arid basins.