As a core component of an aero-engine, the aerodynamic performance of the nacelle is essential for the overall performance of an aircraft. However, the direct design of a three-dimensional (3D) nacelle is limited by the complex design space consisting of different cross-section profiles and irregular circumferential curves. The deep manifold learning-assisted geometric multiple dimensionality reduction method combines autoencoders (AE) with strong capabilities for non-linear data dimensionality reduction and class function/shape function transformation (CST). A novel geometric dimensionality reduction method is developed to address the typical constraints of nacelle parameterization. Low-dimensional latent variables are extracted from the high-dimensional design space to achieve a parametric representation of 3D nacelle manifolds. Compared with traditional parametric methods, the proposed geometric dimensionality reduction method improves the accuracy and efficiency of geometric reconstruction and aerodynamic evaluation. A multi-objective optimization framework is proposed based on deep manifold learning to increase the efficiency of 3D nacelle design. The Pareto front curves under drag divergence constraints reveal the correlation between the geometry distribution and the surface isentropic Mach number distribution of 3D nacelles. This paper demonstrates the feasibility of the proposed geometric dimensionality reduction method for direct multi-objective optimization of 3D nacelles.