The threat of North Korea's long-range firepower is recognized as a typical asymmetric threat, and South Korea is prioritizing the development of a Korean-style missile defense system to defend against it. To address this, previous research modeled North Korean long-range artillery attacks as a Markov Decision Process (MDP) and used Approximate Dynamic Programming as an algorithm for missile defense, but due to its limitations, there is an intention to apply deep reinforcement learning techniques that incorporate deep learning. In this paper, we aim to develop a missile defense system algorithm by applying a modified DQN with multi-agent-based deep reinforcement learning techniques. Through this, we have researched to ensure an efficient missile defense system can be implemented considering the style of attacks in recent wars, such as how effectively it can respond to enemy missile attacks, and have proven that the results learned through deep reinforcement learning show superior outcomes.