Motivated by the observation that vortex flow structure was evident in the energy loss at the surcharged junction manhole due to changes of hydraulic and geometrical parameters, a physical model was used to calculate energy loss coefficients and investigate the relationship between flow structure and energy loss at the surcharged three-way junction manhole. The effects of the flow discharge ratio, the connected angle between two inflow pipes, the manhole geometry, and the downstream water depth on the energy loss were analyzed based on the quantified energy loss coefficients and the identified flow structure. Moreover, two empirical formulae for head loss coefficients were validated by the experimental data. Results indicate that the effect of flow discharge ratio and connected angle are significant, while the effect of downstream water depth is not obvious. With the increase of the lateral inflow discharge, the flow velocity distribution and vortex structure are both enhanced. It is also found that a circular manhole can reduce local energy loss when compared to a square manhole. In addition, the tested empirical formulae can reproduce the trend of total head loss coefficient.