The study investigated the effect of commissural alignment on the depth and clinical outcomes of transcatheter aortic valve implantation (TAVI) using multidetector helical CT. Patients were divided into aligned (0–30° commissural shift, n = 106) and malaligned (>30° shift, n = 109) groups based on pre- and post-procedure CT. Primary endpoints included implantation depth, left ventricular ejection fraction (LVEF), 30-day complications, and quality of life as measured by the TASQ questionnaire. Misaligned patients had greater implantation depth (p = 0.035) and larger left coronary cusps (5.21 ± 0.64 mm vs. 4.92 ± 0.41 mm, p < 0.001), with a higher rate of deep implantation (>10 mm: 9.17% vs. 1.89%, p = 0.020). They had more frequent complications: paravalvular leak (19.27% vs. 6.60%, p = 0.006), pacemaker implantation (11.93% vs. 3.77%, p = 0.027), and valve dislocation (15.60% vs. 5.66%, p = 0.018). Aligned patients achieved better 1-month TASQ scores (76.65 ± 17.31 vs. 69.85 ± 16.41, p = 0.003), especially in physical limitations (p = 0.004) and emotional impact (p = 0.013).