Quantifying the effects of hydrothermal fluctuation and land cover changes on vegetation net primary productivity (NPP) is of great significance for the terrestrial carbon cycle and its driving mechanisms. Based on time-series NPP and land cover data derived from the Moderate Resolution Imaging Spectroradiometer (MODIS), as well as ground-based meteorological data including monthly mean air temperature and precipitation, this study quantified the spatial and temporal changes of vegetation NPP from 2000 to 2015 in Northeast China using the methods of correlation, regression, and spatial analysis. Meanwhile, the relative effects of hydrothermal fluctuation and land cover changes on vegetation NPP were examined. The results showed that the annual NPP increased with fluctuations, from 369.24 g C m^-2 a^-1 in 2000 to 453.84 g C m^-2 a^-1 in 2015, averaging 412.10 g C m^-2 a^-1 over the past 16 years in Northeast China. Overall, vegetation NPP increased at the annual rate of 4.54 g C m^-2 a^-1 during the study period. Spatially, vegetation NPP values were relatively higher in the east and south areas of Northeast China than those in the west and north areas, respectively. In the whole study region, a slight increase in NPP dominated the NPP expansion trend, accounting for 45.9% of the total study area. There were evident discrepancies in the values of average annual NPP among various land cover types from 2000 to 2015 in Northeast China, with the highest NPP of 400.34 g C m^-2 a^-1 for shrubland and the lowest NPP of 300.49 g C m^-2 a^-1 for grassland. The annual NPP was distinctively correlated with two hydrothermal fluctuation factors during the study period. The correlation between NPP and temperature was not significant, whereas NPP was positively correlated with precipitation. Hydrothermal fluctuation factors made a larger contribution to the total NPP changes of different land cover types than did the change in land cover from 2000 to 2015 in Northeast China, with respective contribution rates of over 70% for both forest and cropland.