Water deficit is an important basis for regional wet and dry climates. Based on daily observation data of 63 meteorological stations in Huaihe River Basin from 1957 to 2014, the cumulative departure, Mann-Kendall mutation analysis, Morlet wavelet analysis and ArcGIS inverse distance weight spatial interpolation were used to calculate the water deficit in the Huaihe River Basin periodic characteristics and temporal and spatial distribution characteristics and to analyze the main influencing factors. The results show that:(1) The distribution of water deficit in the region basically meets the lowest in May and the highest in July. (2) According to the seasonal distribution, the area proportion of water deficit sequencially as follows autum, spring, winter, and summer, the strongest in spring. According to the distribution of muti-average water deficit, water deficit decreases from south to north. Regardless of season or muti-average status, there is a lagging effect of mountain and river on the north-south decreasing of water deficit. (3) According to the temporal-spatial distribution of climatic propensity factors of various factors, in southeastern of Jiangsu, western of Shandong, most areas of Henan, and the middle Hubei, the predominant factor of the variation of water deficit is evapotranspiration while the dominant factor of other regions is rainfall. (4) The water deficit in the Huaihe river basin has periodic characteristics, and the first main cycle is 10 years.