To improve the scientific management capacity of water resources in Harbin priority control section in Songhua River Basin, SWAT model was used to simulate the spatial and temporal characteristics of the water resources. Results show that the spatial and temporal distribution of the water resources in the study area was uneven. The runoff during the flood season was the largest, accounting for 56% of the annual runoff, while that of the dry season was only 16.1% of the annual runoff. The inter-annual runoff ranged from 725 to 2 872 m³/s and the average runoff was 1 320 m³/s. The monthly precipitation in the study area showed a significant upward trend in June and August. The spatial distribution of water resources in sub-basins was different in the years of abundance, normality, and dryness that sub-basins 20 and 23 had greater contributions to the water resources. The contribution rates of runoff in the sub-basin 20 were the highest in the years of abundance, normality, and dryness, which were 10.46%, 8.2% and 11.31%, respectively. The Harbin priority control section was further divided into eight ecological function zones based on the characteristics of water resource sensitivity of sub-basins. Water resources management and utilization plan were proposed combined with objectives of the function zones. The results of this study provide technical guidance for the management and utilization of regional water resources.