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A major disturbance in nature, drought, has a significant impact on the vulnerability and resilience of semi-arid ecosystems by shifting phenology and productivity. However, due to the various disturbance mechanisms, phenology and primary productivity have remained largely ambiguous until now. This paper evaluated the spatio-temporal changes of phenology and productivity based on GIMMS NDVI3g time series data, and demonstrated the responses of vegetation phenology and productivity to drought disturbances with the standardized precipitation evapotranspiration index (SPEI) in semi-arid ecosystems of northern China. The results showed that (1): vegetation phenology exhibited dramatic spatial heterogeneity with different rates, mostly presented in the regions with high chances of land cover type variation. The delayed onset of growing season (SOS) and advanced end of growing season (EOS) occurred in Horqin Sandy Land and the eastern Ordos Plateau with a one to three days/decade (p < 0.05) rate and in the middle and east of Inner Mongolia with a two days/decade rate, respectively. Vegetation productivity presented a clear pattern: south increased and north decreased. (2) Spring drought delayed SOS in grassland, barren/sparsely vegetated land, and cropland, while autumn drought significantly advanced EOS in grassland and barren/sparsely vegetated lands. Annual drought reduced vegetation productivity and the sensitivity of productivity regarding drought disturbance was higher than that of phenology.