Considering the issues of water scarcity, water environment deterioration, and unreasonable allocation of water resources in the urban area of the Yellow River Basin, this paper introduces the human–water harmony theory to the allocation of regional water resources. Based on an analysis of the structural characteristics of the regional water resource system, the harmonious water resource allocation (HWRA) model—which includes three sub-systems (i.e., the water service system, ecological environmental system, and economic and social system)—is established. In addition, considering the uncertain factors in the HWRA model, the inexact fuzzy multi-objective programming (IFMOP) method is used to solve the model, aiming at achieving the minimum amount of regional water scarcity, the minimum amount of sewage discharge, and the maximum total economic benefit. A case study of water resource allocation of Binzhou, a city located in the Yellow River Basin, is conducted to validate the model. The model solution results show that the water resource system in Binzhou in 2025 and 2035 could be optimized after harmonious allocation, especially in terms of the water service and ecological environmental systems. Compared with the optimal water resource allocation (OWRA) model, the HWRA model has a more scientific water supply structure, and a smaller amount of sewage discharge. The HWRA model solves the variables using an interval number, so it can flexibly and scientifically reflect the decision-making process.