Current successes in artificial intelligence domain have revitalized interest in spacecraft pursuit-evasion game, which is an interception problem with a non-cooperative maneuvering target. The paper presents an automated machine learning (AutoML) based method to generate optimal trajectories in long-distance scenarios. Compared with conventional deep neural network (DNN) methods, the proposed method dramatically reduces the reliance on manual intervention and machine learning expertise. Firstly, based on differential game theory and costate normalization technique, the trajectory optimization problem is formulated under the assumption of continuous thrust. Secondly, the AutoML technique based on sequential model-based optimization (SMBO) framework is introduced to automate DNN design in deep learning process. If recommended DNN architecture exists, the tree-structured Parzen estimator (TPE) is used, otherwise the efficient neural architecture search (NAS) with network morphism is used. Thus, a novel trajectory optimization method with high computational efficiency is achieved. Finally, numerical results demonstrate the feasibility and efficiency of the proposed method.