Based on the characteristics of large flow rate, low head, short annual operation time, and high reliability of the city flood-control pumping stations, a new-type shaft tubular pumping system featuring a shaft suction box and a siphon-type discharge passage with a vacuum breaker as the cutoff device was developed, which possesses such advantages as simple structure, reliable cutoff, and high energy performance. Taking some pumping stations as the case studies, in the light of the specified operation conditions, the hydraulic optimal design of the shaft-type tubular pumping system was determined and the optimized shape of the system was recommended. The performance prediction based on the computational fluid dynamics methodology was determined and the model test verification was conducted. The results show that the predicted data agree with the experimental head and efficiency so that both methods can be used to determine the performance of a real pumping station. Finally, the in-situ measurements of a pumping station during the commissioning period further verified that the shaft-type tubular pumping station with a siphon discharge passage is of higher efficiency, more reliable and stable.