Huai River Basin, as the sixth largest river basin in China, has a high-regulated river system and has been facing severe water problems. In this article, the changing patterns of runoff and precipitation at 10 hydrological stations from 1956 to 2000 on the highly regulated river (Shaying River) and less-regulated river (Huai River) in the basin are evaluated at the monthly, seasonal and annual scales using the Mann-Kendall test and simple linear regression model. The results showed that: (1) No statistically significant trends of precipitation in the upper and middle Huai River Basins were detected at the annual scale, but the trend of annual runoff at Baiguishan, Zhoukou and Fuyang stations in Shaying River decreased significantly, whereas the others were not. Moreover, the decreasing trends of runoff for most months were significant in Shaying River, although the trend of monthly precipitation decreased significantly only in April in the whole research area and the number of months in the dry season having significantly decreasing trends in runoff was more than that in the wet season. (2) The rainfall-runoff relationship was significant in both highly regulated river and less-regulated river. In regulated river, the reservoirs have larger regulation capacity than the floodgates and thus have the smaller correlation coefficient and t-value. In Huai River, the correlation coefficients decreased from upper stream to downstream. (3) The regulation of dams and floodgates for flood control and water supply was the principal reason for the decreasing runoff in Huai River Basin, although the decreasing precipitation in April in this basin was statistically significant. The findings are useful for recognizing hydrology variation and will provide scientific foundation to integrated water resources management in Huai River Basin.