To explore the flow structure and head loss at surcharged nodes in the surcharging process, this paper simulated 87 cases with different boundary conditions using three-dimensional structural model based on the experimental pipeline node model. Comparison validation between the indoor experiment and the numerical simulation was completed. Qualitative and quantitative analysis, data correlation fitting and π theory were used to study the effect of diameter ratio (the ratio of node diameter Φ m to pipe diameter Φ p), pipe slope and confined pressure head on the flow structure and local head loss. The results show that the water flow interaction at the node-outlet is the main cause of head loss. The local head loss coefficient K is positively correlated with the diameter ratio, but negatively correlated with surcharging depth and confined pressure head. It is feasible to propose K=f(Re) relation formula by π theory. In addition, the value of K with two diameter ratios has different responses to the pipeline slope change, therefore, the effect of diameter ratio should be considered in the design of pipeline slope. The research results supplement the flow structure in the storm flood model, and can provide empirical values and law reference for the calculation of head loss of one-dimensional pipe network at the nodes.