Nowadays, field pumping test is still the primary way to obtain accurate hydrogeological parameters, and high cost and low efficiency are still its main limitations. Therefore, it is still beneficial to study how to obtain hydrogeological parameters quickly and accurately. In this paper, the Trefftz method is applied in combination with the New Fictitious Time Integration Method（NFTIM）, to solve the groundwater reverse calculation problem with unknown partial boundary and effectively solve the discomfort in the reverse calculation problem. Based on the actual pumping test data of the ZK03 hole in the section V of Harbin Metro Line 3, the model was built. By verifying the analytical solution with the Thiem formula and comparing it with the observation well data, it is proved that the Trefftz inverse calculation method is more operable and has a high degree of accuracy (with average error of 9.94 × 10^–10). Concurrently, the hydrogeological parameters such as the influence radius, water head distribution, and depth drop curve of the pumping well are calculated to provide crucial for the design and construction of subway engineering.