Based on the Malmquist-total factor productivity index decomposition method, this study incorporates marine energy, capital, and labour into a research framework to measure the marine input-biased technological progress index and its bias effect in various coastal regions of China. Through the change in the proportion of factor inputs, this study further judges the bias of the factor allocation of marine technological progress, and systematically investigates the regional differences in the bias of marine technological progress. The results indicate that there is input-biased technological progress in the marine economy, and the biased technological progress in most regions is a stable contributing factor for promoting the improvement of TFP and the development of marine economy. However, with the passage of time, this bias effect is gradually weakened, and China’s marine technological progress is gradually deviating from a reasonable allocation structure. Marine technological progress tends to save labour between capital and labour inputs as well as energy and labour inputs, and tends to save energy between capital and energy inputs, but generally prefers to save labour.