Rapid filling of urban drainage pipelines during intense rainfall can compress entrapped air and trigger pressure surges or geysering when air release through manhole-cover openings is restricted. Unlike studies focusing on simplified pipes or isolated shafts, this work examines the coupled air–water response of a prototype-scale drainage section with drop structures, branch inflows, variable-diameter inverted siphons, multiple shafts, and restricted manhole-cover venting. A three-dimensional unsteady air–water two-phase model was established and applied to nine two-stage inflow scenarios after validation against published rapid-filling pressure data. The results show that hydraulic slugs segmented the continuous crown air layer into localized air pockets and produced a high-pressure concentration zone upstream of the downstream diameter change, with a maximum shaft-top pressure of 29.2 kPa under the representative high-flow condition. In local shafts, insufficient venting through small openings, bottom water sealing, and continuous air supply jointly induced delayed geysering cycles characterized by pressure accumulation, breakthrough, relief, and re-accumulation, with a period of 110–120 s and peak pressures of 19–21 kPa. The second-stage rapid-filling flow rate dominated downstream peak pressures; when it increased from 9 to 11 m³/s, the peak pressure at a representative downstream shaft rose from 16 to 34 kPa. These findings clarify the mechanisms of high-pressure concentration and delayed geysering under restricted venting and support the identification of pressure-sensitive nodes in complex drainage networks.