Background: In secondary mitral regurgitation (SMR), effective regurgitant orifice area by the proximal isovelocity surface area method (EROA{}_{\text{PISA}}) evaluation might cause an underestimation of regurgitant orifice area because of its ellipticity compared with vena contracta area (VCA). We aimed to reassess the SMR severity using VCA-related parameters and EROA{}_{\text{PISA}}. Methods: The three-dimensional transesophageal echocardiography data of 128 patients with SMR were retrospectively analyzed; the following parameters were evaluated: EROA{}_{\text{PISA}}, anteroposterior and mediolateral vena contracta widths (VCWs) of VCA (i.e., VCW{}_{\text{AP}} and VCW{}_{\text{ML}}), VCW{}_{\text{Average}} calculated as (VCW{}_{\text{AP}} + VCW{}_{\text{ML}})/2, and VCA{}_{\text{Ellipse}} calculated as \pi \times (VCW{}_{\text{AP}}/2) \times (VCW{}_{\text{ML}}/2). Severe SMR was defined as VCA \ge0.39 cm{}^2. Results: The mean age of the patients was 77.0 \pm 8.9 years, and 78 (60.9%) were males. Compared with EROA{}_{\text{PISA}} (r = 0.801), VCW{}_{\text{Average}} (r = 0.940) and VCA{}_{\text{Ellipse}} (r = 0.980) were strongly correlated with VCA. On receiver-operating characteristic curve analysis, VCW{}_{\text{Average}} and VCA{}_{\text{Ellipse}} had C-statistics of 0.981 (95% confidence interval [CI], 0.963–1.000) and 0.985 (95% CI, 0.970–1.000), respectively; these were significantly higher than 0.910 (95% CI, 0.859–0.961) in EROA{}_{\text{PISA}} (p = 0.007 and p = 0.003, respectively). The best cutoff values for severe SMR of VCW{}_{\text{Average}} and VCA{}_{\text{Ellipse}} were 0.78 cm and 0.42 cm{}^2, respectively. The prevalence of severe SMR significantly increased with an increase in EROA{}_{\text{PISA}} (38 of 88 [43.2%] patients with EROA{}_{\text{PISA}} 0.30 cm{}^2, 21 of 24 [87.5%] patients with EROA{}_{\text{PISA}} = 0.30–0.40 cm{}^2, and 16 of 16 [100%] patients with EROA{}_{\text{PISA}} \ge0.40 cm{}^2 [Cochran–Armitage test; p 0.001]). Among patients with EROA{}_{\text{PISA}} 0.30 cm{}^2, SMR severity based on VCA was accurately reclassified using VCW{}_{\text{Average}} (McNemar’s test; p = 0.505) and VCA{}_{\text{Ellipse}} (p = 0.182). Conclusions: Among patients who had SMR with EROA{}_{\text{PISA}} of 0.30 cm{}^2, suggestive of moderate or less SMR according to current guidelines, >40% had discordantly severe SMR based on VCA. VCW{}_{\text{Average}} and VCA{}_{\text{Ellipse}} values were useful for identifying severe SMR based on VCA in these patients.