Port logistics data governance is characterized by multi-subject, multi-dimensional and dynamic interaction, which brings significant challenges for enterprises to perform the strategic value of data information. In order to maximize the potential of data information, this paper systematically and quantitatively assesses and optimizes port logistics data governance capabilities through an enhanced Meta-Network Analysis-Simulated Annealing Algorithm (MNA-SAA)-based approach. This approach first applies the MNA method to conceptualize port logistics data governance as “Data Information-Skilled People-Technology-Process” (I-A-T-P) meta-networks, which portray the dynamic interaction behavior of data information between different subjects. Then, multi-level meta-network metrics (i.e., people/process data information waste congruence, data information actual/potential load, organization people data information needs congruence, and perform as accuracy) are used to the port logistics data governance capabilities. The SAA is applied to optimize the data governance structure from the skilled people-data information interaction (AI) network. This proposed approach is validated by a generic port logistics data governance case study. Based on the optimization results of the generic port logistics data governance meta-networks, its data governance capability improvement strategies and the advantages of the enhanced MNA-SAA approach are discussed. Overall, this enhanced MNA-SAA approach promotes an understanding of port data governance by systematically conceptualizing complex data governance structures and quantifying data governance capabilities. This study provides decision-makers with implementable support to advance stakeholder collaboration and knowledge sharing to improve future port logistics data governance capabilities.