This paper aims to solve the decision-making problem of value chain reconstruction of Chinese port enterprises under the background of the Free Trade Zone policy. Based on value chain theory and system dynamics method, this paper constructs a simulation model that can simulate the value-added change process of port enterprises under different combination input conditions. Furthermore, it conducts simulation case studies. The research indicates that the Free Trade Zone policy has a significant promoting effect on the restructuring of port enterprise value chains and the transformation and upgrading of enterprises. Moreover, considering the impact of the Free Trade Zone policy and limited resources, the overall benefits to port enterprises from combined investments are superior to those from single-factor investments. According to the value chain theory, the business segments of a port are decomposed into ancillary value activities, basic value activities, and external value activities. The investments in these three types of value activities play roles, respectively, in enhancing the operational efficiency of port enterprises, expanding the business scope of port enterprises, and strengthening the core competitiveness of port enterprises. From the overall perspective of the system, Shanghai Port can obtain the maximum operating profit when the endogenous factor input rate is 13%, the basic factor input rate is 4%, and the exogenous factor input rate is 13%. The findings of this research provide a decision-making reference for Chinese port enterprises to realize value reconstruction, transformation, and upgrading in the context of the Free Trade Zone policy.