The baffle-drop shaft structure is usually applied in deep tunnel drainage system to transfer shallow storm water to underground tunnels. At present, the definition of the maximum operational capacity of baffle-drop shafts was lack of scientific and reasonable analysis, and the researches on hydraulic and energy dissipation characteristics were insufficient. In this paper, a 1:25 scale hydraulic model test was conducted to observe the flow phenomena during the discharge process, analyze the relationship between the maximum inflow discharge and the baffle parameters, and calculate the energy dissipation rate of the shaft under different ﬂow conditions. The results demonstrated that three kinds of flow regimes were presented in the discharge process: wall-impact confined flow, critical flow, and free-drop flow. The impact wave majorly brought about the energy dissipation of water on the baffle. The impingement and breakup of the inflow at the bottom of the drop shaft, as well as the reverse flow, resulted in the final energy loss. The time-averaged pressure value of the upper baffle was 1.5–3 times that of the central and lower baffles. The baffle with a design angle could effectively reduce the time-averaged pressure of the water flow acting on the baffle. The energy dissipation rate of the drop shaft decreased with the increase in the inflow discharge, and the energy dissipation rate was found to range from about 63.14% to 96.40%. The optimal size of the baffle-drop shaft with the maximum energy dissipation rate was d/B = 0.485 and θ = 10° (d, B, and θ are the baffle spacing, width, and angle, respectively).