The ecological and environmental resources can be reconfigured between countries and regions to a certain extent by ecological inputs and outputs of international trade. While China vigorously develops aquatic products trade, it also faces problems such as the loss of ecological resources. Based on the ecological footprint model, this paper measured the ecological footprint and ecological net value of China's aquatic product trade with 35 major countries and regions from 2001 to 2020. The spatial and temporal evolution characteristics of the ecological net value were revealed through ArcGIS, and the future trend of the changes was predicted by using the ARIMA model. The results showed that: (1) The ecological footprint values of China's aquatic products imports and exports were large, with the significant gap among the ecological footprint values in different types of aquatic product trade. (2) The overall net ecological value trend was unstable although the net ecological net value of China's aquatic product trade had shown a significant upward trend recently. At the meantime, there were large differences in the ecological net value of different types of aquatic product trade. (3) In the temporal dimension, the ecological net value of China's aquatic product trade did not have a high degree of overall change. However, there were obvious problems of heterogeneity, and the degree of concentration changed more obviously in the spatial dimension. (4) The distribution of major countries in the ecological footprint of China's aquatic products export trade and the ecological footprint of China's aquatic products import trade had basically remained stable, but there had been obvious changes in a few major countries. And the concentration of both aquatic products export trade and import trade was relatively high. (5) It was predicted that the ecological footprint of China's aquatic products exports and imports would be in a state of obvious disequilibrium from 2021 to 2025, and the spatial distribution of the ecological net value of China's aquatic product trade in 2025 would still encounter with obvious heterogeneity problems. Therefore, we put forward the relevant countermeasures to optimize the ecological footprint of China's aquatic product trade from different dimensions, such as optimizing the trade structure of aquatic products, smoothing the dual circulation path of industry, enhancing the innovation capacity of marine science and technology, and deepening the cooperation system of multilateral trade. It is hoped to provide a realistic basis for the sustainable development of China's aquatic product trade.