The GRACE satellites data from 2003-2016 in the Huaihe River basin were used to study the long-term spatiotemporal changes of terrestrial water storage anomaly (TWSA). The normalized difference vegetation index (NDVI) generated from MODIS remote sensing satellite was used to analyze the main influencing factors of TWSA, including precipitation, temperature, runoff, vegetation coverage and circumfluence, using the Pearson analysis and set pair analysis (SPA). The results showed that the TWSA in the Huaihe River basin has a clear annual periodicity, and reaches its peak in the early autumn. The TWSA over the south of the basin, especially in Tongbai and Dabie Mountain area increased in 2016, while in the north of the basin, such as Zhengzhou area decreased significantly. The TWSA in Huaihe basin is positively affected by precipitation and runoff and has a low correlation with temperature. Additionally, the influence of local NDVI and circumfluence index on TWSA is relatively small, showing a negative correlation.