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Recent earlier greening trends are believed to enhance terrestrial ecosystem productivity. However, advanced onset of growing season may also deplete soil water in early spring, leading to summer water stress for plant growth. In this study, we linked soil moisture with start of growing season (SGS, represented by day of year) to examine the responses of ecosystem productivity to water stress during 1982-2011 on the Mongolian Plateau. Results showed that, though not significant, earlier SGS has tendency to enhance spring productivity at north part of the study area. Nonetheless, we observed that suppressed summer photosynthesis due to phenology-induced water stress dramatically reduced annual carbon assimilation. Thus, phenology-associated changes in soil moisture have profound potential in regulating seasonal and annual productivity in arid and semi-arid ecosystems. The relationship between SGS and GPP was not observed in more mesic forest ecosystems (R-2 = 0.04, p > 0.10) nor in the agricultural area (R-2 = 0.03, p > 0.10) where practices like irrigation aim to alleviate summer water stress. Therefore, at the scale of the entire study area, earlier growing season did not translate to higher productivity (R-2 = 0.006). On the contrary, advanced SGS aggravated growing-season water stress, which in turn, supressed annual carbon assimilation in water limited area. This mechanism implies the advanced greening trends may not necessarily lead to more carbon uptake in terrestrial ecosystems but rather a carbon loss, especially in the arid and semi-arid regions.