Abstract: The water resources system is closely related to the regional economy. It is more intuitive to use economic value to reflect the losses caused by water system risks such as water resource imbalance and mismatch. In order to evaluate the risk of water resources system through quantitative economic value, this paper firstly constructed the water loss risk economic loss model, and used the EBM model to calculate the water use efficiency, and combined the water price and per capita wage in Heilongjiang Province to determine the water resource risk value. Then, based on the EBM, a two-stage Tobit model was added to analyze the causes of the risk economic loss of the water resources system. The results show that the least economic loss caused by insufficient water resources investment in Heilongjiang Province from 2000 to 2020 is 7.52 billion yuan (2008), the highest is 42.51 billion yuan (2013); the economic loss of minimum output of water resources is 111.9 billion yuan (2000), the highest is 1 106.8 million yuan (2012). From 2000 to 2015, the economic loss of water resources in Heilongjiang Province increased year by year, and the economic loss of water resources output accounted for more than 90% of the economic loss of water resources system. It is estimated that the economic loss of water resources risk in 2020 is 813.87 billion yuan. Jixi, Suihua, Qiqihar, Harbin, Daqing, Jiamusi, Shuangyashan, Qitaihe and Hegang have lower economic losses caused by input and better water resources allocation. The cities with large economic losses caused by output are Yichun, Mudanjiang and Suihua, which require the government to pay more attention to the utilization of water resources in the region. It is necessary to rationally allocate water resources, improve water use efficiency, and reduce the risk economic loss of water resources systems. Hegang, Qitaihe, Jiamusi and other major grain producing areas have greater risk of water resources, greater economic losses and lower water use efficiency. In general, the agricultural water use efficiency in Heilongjiang Province is low, and the phenomenon of flood irrigation is still serious. It is necessary for the government and farmers to cooperate with each other to improve water use efficiency. During the research period, the risk economic loss of water resources system in Heilongjiang Province was large, and the water use efficiency was low. The water use efficiency in most areas was only in the medium range. From the perspective of spatial distribution, water use efficiency is high in the north-south direction and low in the east-west direction. The water use efficiency in the eastern region is lower than that in the other regions. The water resources system of Heilongjiang Province is affected by industrial structure, per capita GDP, per capita water resources and water resources investment. Water price is correlated with water use efficiency in only a few cities, indicating that the government's purpose of regulating water resources through water prices has not been met, and the government needs to introduce relevant policies to change in the future. This article will support the development of risk aversion measures for subsequent water resources systems.