As an important component of water supply networks, the H-junctions exhibit unclear characteristics of income-flow incomplete mixing. This paper investigates the phenomena and influencing factors of incomplete mixing at H-junctions within water supply networks, intending to improve existing water quality simulation techniques. By combining computational fluid dynamics (CFD) numerical simulations and laboratory experiments, the effects of various factors such as pipe diameter, spacing of tees, and inlet and outlet Reynolds number ratios on incomplete mixing at H-junctions were explored. The findings suggested that while pipe diameter has minimal influence on mixing, spacing of tees and inlet/outlet Reynolds number ratios significantly affect the degree of mixing. Moreover, the experimental results aligned well with CFD simulations, validating their accuracy and providing data for establishing an empirical model for incomplete mixing at H-junctions under different spacings of tees. Ultimately, an empirical model for H-junction incomplete mixing based on the specific spacing of tees conditions was proposed. Selecting appropriate mixing models in practice to enhance the accuracy of water quality simulations in water supply networks was recommended, which is crucial for ensuring water safety and optimizing operational scheduling.