Water is one of the limiting factors that impact the agricultural production in the black soil region in Northeast China. The seasonal drought caused by the uneven distribution of precipitation threatens crop yield in this region. The objective of this study was to examine if different fertilization treatments would affect soil water supply, then mitigate the impact of seasonal drought on crop yield. A long-term experiment was conducted at the National Field Research Station of Agro-ecosystem in the Chinese Academy of Science in Hailun County in Heilongjiang province in Northeast China from 2005 to 2008. Three fertilizer treatments including no fertilizer (CK), chemical fertilizer (NP) and chemical fertilizer plus pig manure (NPM) were tested. The results showed that crop received chemical fertilizer plus pig manure had the largest evapo-transpiration (ET) in observed four-years followed by NP and CK, which resulted in soil water storage (0-170 cm) showed a decreasing trend of CK > NP > NPM during the growing seasons. Water stored in the soil profile was one of the most important sources for crop water consumption. Crops in NPM and NP treatments could utilize more water stored in soil profile, by 41.52% and 24.94%, respectively, compared with CK. The yield and water use efficiency of maize and soybean in NPM were higher than that in NP and CK, suggesting that utilized soil water could mitigate the effect of seasonal drought on crop yield. Therefore, NPM was a viable management practice in the black soil zone in Northeast China for improving soil water supply and crop yields.