Pond aquaculture is a traditional method of mariculture in China, and it is also the main current land-based mariculture. Since the 1970s, seawater pond aquaculture has gone through a development process of extensive, semi-intensive, intensive, and multi-nutrient ecological aquaculture, forming a development pattern of multiple types, modes, and formats. However, there are still key problems in the current pond aquaculture industry, such as unclear ecological adaptability mechanisms of aquaculture organisms, unstable output of aquaculture systems, and low efficiency in nutrient utilization, which seriously restrict the development of pond aquaculture industry. We carried out an analysis of the interaction mechanism between improved varieties of marine aquaculture shrimp and crab and the ecological environment, developed technologies for optimizing the structure of aquaculture ecosystems, efficiently utilizing nutrient resources, established a platform for aquaculture information collection and intelligent control, created a new model of ecological engineering aquaculture, improved the efficiency of nutrient utilization, and achieved efficient and sustainable output of the aquaculture system, which may provide important theoretical basis and technical support for the green and quality development of pond aquaculture industry in China.