Abstract: Groundwater flow velocity in wellbore is usually measured by single-well tracking tests or Aqua Vision flow velocity and direction meters to calculate the groundwater flow velocity in the aquifer. Due to the impact of the skin structure, the groundwater flow field near the wellbore changes, causing a difference between the flow velocity in the wellbore and that in the aquifer. In order to investigate the influence of the skin effect on the groundwater flow velocity in the wellbore, a numerical model of groundwater flow that considers the skin effect was established using the COMSOL Multiphysics software. On this basis, the mechanisms by which the skin thickness and hydraulic conductivity affect the groundwater flow velocity in the wellbore was systematically analyzed and the reliability of the existing empirical formula that converts the groundwater flow velocity in the wellbore into the Darcy velocity in the aquifer was further assessed based on the simulation results. Key finding are as follows: (1) The larger the hydraulic conductivity of the skin area near the wellbore, the greater the groundwater flow velocity in the wellbore, and the relative error of the groundwater flow velocity calculated by the empirical formula is less than 0.23%, showing high reliability. (2) When the hydraulic conductivity of the skin area is smaller than that of the aquifer, the groundwater flow velocity in the wellbore decreases as the skin thickness increases, and the relative error of the empirical formula calculation shows an increasing trend. (3) When the hydraulic conductivity of the skin area is larger than that of the aquifer, the groundwater flow velocity in the wellbore increases as the skin thickness increases, and the relative error of calculation shows a decrease trend in general, but its error volatility is large, indicating that the stability of the empirical formula calculation under this condition is poor. In conclusion, the skin structure has a great influence on the water flow rate inside the wellbore, and the influence of skin structure should be concerned in practical projects.