Due to the quality and error of the data itself, historical automatic identification system (AIS) data was insufficient used to predict navigation risk at sea, but it adequately used to train decision-making neural networks. This paper presents a real AIS ship navigation environment with a rule-based and a neural-based decision processes with frame motion and training the decision network using a deep reinforcement learning algorithm. Rule-based decision-making has several applications in the field of adaptive systems, expert systems, and decision support systems, it also including general ship navigation which regulated by the convention on the international regulations for preventing collisions at sea (COLREGs). However, if someone intend to achieve full unmanned ship navigation without any remote control at the open sea, a rule-based decision-making system cannot be implemented alone. With the growing amount of data, complex sea environment, different collision scenarios, the agent-based decision has become an important role in transportation. For ships, combined rule-based and neural-based decision-making is the only option. It has become progressively challenging to satisfy autonomous decision-making development requirements. This study uses deep reinforcement learning to evaluate the performance of decision-making efficiency under different AIS data input shapes. The results show that the decision neural network trained with AIS data has good robustness and a high ability to achieve collision avoidance. Furthermore, using the same methodology, include instructive guidance for processing radar, camera, ENC, etc., respond to different risk perception tasks in different scenarios. It has important implications for fully unmanned navigation.