At present, underfilling or overfilling the volume of the balloon-expandable transcatheter heart valve (THV) is generally utilized in transcatheter aortic valve implantation (TAVI). However, no research has assessed the clinical impact of filling volume variations of the current-generation SAPIEN 3 THV. We analyzed the clinical data of 331 patients who underwent TAVI with SAPIEN 3 at our institution. Post-procedural echocardiographic and multidetector computed tomography (MDCT) scan data and 3-year prognoses according to each filling volume were assessed. The procedural outcomes and 3-year mortality rates were comparable among the underfilling, nominal filling, and overfilling groups. For all THV sizes, the THV area evaluated on post-procedural MDCT scan increased stepwise along with an elevated filling volume, thereby covering a wide range of native annulus area. Compared with patients in the nominal filling and overfilling groups, those with 23-mm THVs in the underfilling group had a smaller effective orifice area (EOA) (1.38 [IQR: 1.18–1.56] vs. 1.57 [IQR: 1.41–1.84] vs. 1.58 [IQR: 1.45–1.71] cm², P = 0.02) and a higher mean transvalvular gradient (13.6 [IQR: 11.0–15.7] vs. 12.1 [IQR: 9.0–14.9] vs. 12.0 [IQR: 8.1–14.8] cm², P = 0.04). In conclusion, by adjusting the filling volume of SAPIEN 3 using THV with limited sizes, continuously distributed native annulus areas were covered. The underfilling implantation technique had a minimal negative effect on the valve function of 23-mm THVs only. In the entire cohort, the filling volume variations did not affect the mid-term prognosis negatively.