Currently, marine security is becoming increasingly severe, with incidents of harassment, attack, and sabotage against vessels occurring frequently. Aquaculture vessels, operating long-term in deep seas, are particularly susceptible to various forms of harassment, attack, and sabotage, which seriously threaten their safe operation. Additionally, aquaculture vessels also face significant internal security risks. It is therefore necessary to establish a complete security system for the aquaculture vessels to ensure their safe operation. The potential security risks are categorized into external risks and internal risks based on the characteristics of an aquaculture vessel. Accordingly, it constructs the external and internal risk security systems, clarifies the overall composition and workflow of the external security system, and establishes a “scenario-personnel” double closed-loop laboratory security system, as well as proposes specific security measures against violent and terrorist crimes. From the perspectives of monitoring, emergency, and supervision, an integrated security system is established to ensure the safe operation of aquaculture vessels.