This study examines the impact of axial clearance variations on the performance characteristics of a dual-rotor flowmeter (DRT-FM) through numerical simulations, with the validity of the numerical results verified by calibration experiments. The results indicate that within the range of 200 L/h to 1600 L/h, the K factors of different groups increase as clearance increases. The K factor of the 0.80 mm group is the largest, showing an average increase of around 6% compared to that of the 0.50 mm group. Additionally, Linearity E also decreased, with a minimum of 1.07% in the 0.65 mm group, significantly lower than the 3.33% in the 0.50 mm group. Furthermore, the pressure loss increased slightly, with the 0.65 mm group having the largest pressure loss; however, at a flow rate of 1600 L/h, the pressure loss only increases by 0.186 kPa compared to that of the 0.50 mm group. Flow field analysis reveals that changes in axial clearance predominantly affect pressure distribution. Larger clearances reduce low-pressure regions on upstream and downstream transition surfaces, thereby reducing energy loss due to pressure changes. Entropy analysis further demonstrates that higher axial clearance decreases energy loss in the upstream and downstream stationary domains, optimizing the DRT-FM’s energy characteristics.