Based on the micro-data of 79 listed companies in the Chinese marine ship industry chain from 2015 to 2019, this paper calculates the comprehensive technical efficiency (TE), pure technical efficiency (PTE), and scale efficiency (SE) of the upstream, midstream, and downstream of China’s marine ship industry chain by using a three-stage super-efficiency slacks-based model (SBM), and further analyzes the weak links in industrial chain efficiency and their influencing factors. It is shown that (i) the TE and PTE of the upstream, midstream, and downstream of China’s marine ship industry chain are in a “V”-shaped distribution, high at both ends and low in the middle, but that the SE is ranked as follows: upstream > midstream > downstream. In addition, the PTE is the main factor which hinders the improvement of TE in the industrial chain. (ii) The environmental variables have significant impacts on industrial chain efficiency. When the influences of environmental variables and random error terms are excluded, the industrial chain efficiency changes significantly. The values of SE and TE decrease significantly, and the distribution characteristic of TE changes. However, the PTE is still in a “V”-shaped distribution and appears to be the main driving force for the progress of TE. (iii) China’s marine ship industry chain has obvious weak links in terms of efficiency, and the midstream and downstream areas need to focus on development. Each link of the industry chain has high coupling and low coordination, and they are all closely related to each other, but the coordination ability is insufficient. The industrial chain in terms of efficiency and coordinated development can still be improved.