Background: Body composition could help to better define the prognosis of cancers treated with anti-angiogenics. The aim of this study is to evaluate the prognostic value of 3D and 2D anthropometric parameters in patients given anti-angiogenic treatments. Methods: 526 patients with different types of cancers were retrospectively included. The software Anthropometer3DNet was used to measure automatically fat body mass (FBM3D), muscle body mass (MBM3D), visceral fat mass (VFM3D) and subcutaneous fat mass (SFM3D) in 3D computed tomography. For comparison, equivalent two-dimensional measurements at the L3 level were also measured. The area under the curve (AUC) of the receiver operator characteristics (ROC) was used to determine the parameters’ predictive power and optimal cut-offs. A univariate analysis was performed using Kaplan–Meier on the overall survival (OS). Results: In ROC analysis, all 3D parameters appeared statistically significant: VFM3D (AUC = 0.554, p = 0.02, cutoff = 0.72 kg/m2), SFM3D (AUC = 0.544, p = 0.047, cutoff = 3.05 kg/m2), FBM3D (AUC = 0.550, p = 0.03, cutoff = 4.32 kg/m2) and MBM3D (AUC = 0.565, p = 0.007, cutoff = 5.47 kg/m2), but only one 2D parameter (visceral fat area VFA2D AUC = 0.548, p = 0.034). In log-rank tests, low VFM3D (p = 0.014), low SFM3D (p < 0.0001), low FBM3D (p = 0.00019) and low VFA2D (p = 0.0063) were found as a significant risk factor. Conclusion: automatic and 3D body composition on pre-therapeutic CT is feasible and can improve prognostication in patients treated with anti-angiogenic drugs. Moreover, the 3D measurements appear to be more effective than their 2D counterparts.