Safety is the premise of efficiency and effectiveness in the port operation. Safety investment is becoming a vital part of port operation in current era in order to overcome different types of hazards the port operation exposed to. This paper aims to improve the safety level of port operation through analyzing its influencing factors and exploring the interactions between the safety investment and system risk level. By analyzing the key factors affecting the port operation and their mutual relationship within a man−machine−environment−management system, a decision-making model of safety investment in port enterprise was established by system dynamics (SD). An illustration example and a sensitivity analysis were carried out to justify and validate the proposed model. The results show that increasing the total safety investment of port enterprises, improving the safety management investment on personnel, and strengthening the implementation effect of investment can improve the degree of port security to a certain extent. The strength of the proposed work is its practical application in current scenarios using real time data and the ability to provide a baseline approach for port enterprises to formulate safety investment strategy.