Pumping stations have been limited to a single functionality, large land occupation, high energy consumption, and low adaptability to fragmented, small-scale paddy fields. Conventional irrigation and drainage can also rely on separate sets of equipment in most rice-growing regions, leading to messy layouts, low utilization efficiency, and high infrastructure costs. Moreover, the irrigation and drainage pumping equipment can be integrated to meet the full cycle water requirements of rice at various growth stages. Water conservancy facilities have been severely restricted in water saving and modern agriculture. This study aims to construct a compact, high-efficiency, and easy-to-deploy small-scale two-way flow passage pumping station, according to the actual water supply and drainage demands of small and medium-sized paddy fields. Stable bidirectional water conveyance without impeller reversal was realized to improve overall hydraulic performance with low land occupation and energy loss. A practical and reliable piece of equipment was provided for precise water in paddy fields. A modular outdoor cabinet structure was adopted with a footprint of only 2.79 m², for easy installation, migration, and maintenance with the minimum occupation of cultivated land. Flexible and reliable switching was achieved among four operating modes—pumping irrigation, pumping drainage, gravity irrigation, and gravity drainage. A unidirectional impeller and five groups of motorized valves were regulated to reduce the mechanical wear under frequent impeller reversal. Numerical simulations were conducted on the Shear Stress Transport (SST) turbulence model using ANSYS 2024 CFX software. Grid independence verification was completed with approximately 5.88 million elements for high computational accuracy and reliability. Internal flow fields were analyzed using velocity vector contours, static pressure contours, external characteristic curves, and quantitative hydraulic loss decomposition. In addition, the hydraulic loss was calculated using the Colebrook-White formula. Field experiments in actual paddy fields were combined to verify simulation accuracy and then evaluate real operational stability and efficiency. Numerical results indicated that the pumping station achieved a peak irrigation efficiency of 59.46% at a flow rate of 28 m³/h, with a head of 16.40 m and shaft power of 2.20 kW. The drainage efficiency reached 50.20% under the same flow condition, with a head of 14.76 m and shaft power of 2.23 kW. The drainage mode shared significantly stronger flow turbulence, more intensive vortex structures, and higher hydraulic loss, compared with the irrigation condition. The mismatch between inflow direction and impeller inlet angle also led to premature flow separation, local flow resistance, and aggravated energy dissipation. Hydraulic loss analysis revealed that the local resistance loss accounted for more than 80% of the total hydraulic loss under irrigation and over 92% under drainage. The energy consumption was attributed to the local pipe fittings, turning sections, and blind tubes. Field experimental results demonstrate that the pumping station operated stably within the flow range of 22.7−40.8 m³/h. The measured irrigation efficiency was 56.67%, and drainage efficiency was 52.15% at the optimal operating point of 28 m³/h, with the relative errors of 4.92% and 3.74%, respectively, compared with numerical simulation, indicating excellent consistency between simulation and test. The pumping station was used to realize the irrigation or drainage operation for 0.2 hm² of paddy field within 3 hours, fully meeting the rapid and efficient water regulation demands of small-scale farmland. The two-way flow passage pumping station was featured by the compact structure, flexible mode switching, stable operation, and high efficiency during the whole growth period, fully meeting the irrigation drainage requirements of paddy fields. Further performance should optimize the flow path to reduce the local resistance for the valve layout and inlet impeller matching. The internal flow and hydraulic loss of the two-way flow passage under bidirectional operation can provide the key technical support and engineering reference for the structure, performance, and large-scale popularization of small-scale irrigation drainage equipment. The finding can contribute to the farmland water saving and the high-quality rice cultivation in modern agriculture.