Enhancing the marine carrying capacity (MCC) is of important value in hastening the transformation of the marine economy and realising the marine economy high-quality development (MEHD). We explore the synergistic mechanism between the MCC and MEHD and its comprehensive indicator system, measure the synergistic relationship between China’s MCC and MEHD from 2006 to 2020 using the improved TOPSIS model and the composite system synergism model, and explore the influencing factors and their interactions using geographic probes. The research findings are (1) that China’s MCC and MEHD show a growing trend during the study period, in which marine green development is at a higher level and the cultivation of marine knowledge improves most significantly, but the general value of the MEHD is relatively low. (2) In terms of the synergistic relationship, the degree of ordering of the two shows a sustained rising trend, and the degree of ordering of the marine economy development as a whole is higher than the MCC; the degree of synergy is increasing, but the general value of synergistic development is low. (3) The main factors driving the MCC and MEHD are the marine consumption capacity, the marine opening, and the marine industrial structure; the explanatory power of most factor interactions tends to decrease, and the explanatory power of the interactions among the development of land-based economy, the marine industry structure, and the marine economy increase, and the impacts of the different factor interactions on the synergistic development are all greater than the factors. The influence of different factors on synergistic development is greater than the influence of each factor alone.