Abstract The pressure surges for water filling in deep stormwater storage tunnels (DSSTs) with entrapped air-pockets seriously threaten the safety of pipeline structures and even lead to the destruction of urban water infrastructure. Hence, this paper develops a volume of fluid (VOF) model to study pressure surges in a two shafts and one tunnel system. Research works under different initial air-pocket parameters are carried out, while the VOF model is verified by the empty tunnel water filling experiment in the same system. The results show that the maximum pressure increases with an initial length/diameter ratio decrease or air volume fraction increase. Also, the extreme pressure with entrapped air-pocket at a certain scale can reach 1.6 times the static pressure (30 m). With the increase of initial air volume fraction, the frequency of pressure surges slows down, while the maximum pressure gradually increases and approaches a specific value within a fixed air volume fraction range (0.2–5.0%). The maximum pressure of air-pocket at different initial positions shows a downward trend from the middle of the tunnel to two sides, while the pressure of the air-pocket near a higher shaft will be slightly higher. The proposed model can be extended to systems with multiple shafts or air-pockets, and the conclusions have reference significance for structure design and water filling control in the DSST.