The development of China’s marine food production system is receiving increasing attention, as its developmental level and obstacle factors will profoundly impact the nation’s future food security and nutritional supply. This study establishes a theoretical framework for evaluating the development level of marine food production systems based on three dimensions—resources, benefits, and governance—structured around the logical framework of “exogenous safeguard, endogenous drive, goal oriented”. First, a three-tier coding method based on grounded theory was employed to construct a Chinese marine food production system evaluation framework encompassing 28 specific indicators. Subsequently, a comprehensive weighting of these indicators was achieved by integrating fuzzy comprehensive evaluation with the entropy weighting method. Finally, based on the evaluation results and obstacle degree modeling, a comprehensive assessment study was conducted on 11 coastal provinces and cities, focusing on developmental level investigation and obstacle factor analysis. The results indicate that China’s marine food production system development level exhibits a trend of slow, fluctuating growth overall, maintaining an average annual growth rate of 3.23%. However, significant differentiation characteristics are emerging, with high regional heterogeneity and substantial variation in obstacle factors. Currently, the main constraints hindering the development of the marine food production system are insufficient human resource supply, uneven production resource distribution (higher in the north, lower in the south), and intensified fluctuations in comprehensive output. Finally, this study proposes three strategic recommendations: ecological restoration coupled with strict controls, comprehensive restructuring of the human resource support system, and establishing a multi-scale comprehensive evaluation mechanism. These strategies aim to disrupt the transmission mechanisms of different obstacle factors and accelerate the rapid development of the marine food production system.