With the increasing running speed, the aerodynamic issues of high-speed trains are being raised and impact the running stability and energy efficiency. The optimization design of the head shape is significantly important in improving the aerodynamic performance of high-speed trains. Existing aerodynamic optimization methods are limited by the parametric modeling methods of train heads which are unable to accurately and completely parameterize both global shapes and local details. Due to this reason, they cannot optimize both global and local shapes of train heads. In order to tackle this problem, we propose a novel multi-objective aerodynamic optimization method of high-speed train heads based on the partial differential equation (PDE) parametric modeling. With this method, the half of a train head is parameterized with 17 PDE surface patches which describe global shapes and local details and keep the surface smooth. We take the aerodynamic drag and lift as optimization objectives; divide the optimization design process into two stages: global optimization and local optimization; and develop global and local optimization methods, respectively. In the first stage, the non-dominated sorting genetic algorithm (NSGA-II) is adopted to obtain the framework of the train head with an optimized global shape. In the second stage, Latin hypercube sampling (LHS) is applied in the local shape optimization of the PDE surface patches determined by the optimized framework to improve local details. The effectiveness of our proposed method is demonstrated by better aerodynamic performance achieved from the optimization solutions in global and local optimization stages in comparison with the original high-speed train head.