Mariculture areas are an important non-renewable natural resource and continuously improving their efficiency is important for increasing mariculture output and adjusting its structure. The aim of this study was to measure the mariculture area production efficiency (MAPE) considering undesirable outputs, further analyze its spatiotemporal disparities, and analyze the reasons for the differences observed during the period from 2008 to 2019. The super-efficiency Engel–Blackwell–Miniard (S-EBM) model and global Malmquist–Luenberger (GML) index was selected to analyze the technical efficiency and productivity of MAPE from both the static and dynamic aspects, and the Theil index was used to decompose the regional differences. The results showed that the MAPE showed fluctuation and an increasing trend overall; the production efficiency and technical progress showed a fluctuating rising trend, and technical progress had a significant driving effect on the production efficiency; and intra-regional differences were the main factors that cause the differences in MAPE. The findings suggest the increase of scientific and technological investment in mariculture, changes in mariculture methods, the establishment of environmental monitoring centers in mariculture areas, and the sharing of information technology between regions to achieve sustainable development.