Nitrous oxide (N2O) is one of the three important greenhouse gases, which has an important impact on atmospheric environment, such as global warming, acid rain formation, ozone layer destruction and so on. As a special artificial aquatic ecosystem, aquaculture, which is rich in nutrients due to the application of a large amount of food, becomes a potential source of nitrous oxide. The total area and increasing rate of aquaculture in the coastal areas of China ranked first in the world, and the emission of N2O from the aquaculture attracted more and more attention. In order to differentiate the production process of N2O and its contribution to the total N2O production of sediment, this study took the reclamation shrimp ponds of Min River estuary in the southeast coast of China as the research object and adopted the laboratory-incubated experiments by means of inhibited process. On this basis, the influence of physicochemical properties on N2O production of sediment was analyzed and the measures to reduce N2O emission from the aquaculture were put forward. Results showed that the average N2O production rate of sediment from the shrimp pond was 1.80, 5.95 and 8.70 nmol/( kg·h) in the early, middle and final stages of the aquaculture, respectively. The shrimp pond was the N2O sources and the production rate increased with the time of aquaculture. The mean contribution of nitrification, denitrification, nitrifier denitrification and abiotic effect in the three aquaculture period was -162.04%, 327.52%, -239.45% and 90.27%, respectively. The N2O production of the sediments from the shrimp ponds in Min River estuary was generated from the denitrification and abiotic effect, while nitrification and nitrifier denitrification played a negative role. Nitrification was negatively correlated with denitrification and nitrifier denitrification, while nitrifier denitrification was negatively correlated with abiotic effect. The total N2O production rate of sediments in the shrimp ponds increased with temperature and decreased with salinity in general, which reached the maximum under the high-temperature and low-salinity condition and the minimum under the low-temperature and high-salinity condition. Salinity had a significant effect on the total N2O production and the four different production processes, while the interaction of temperature and salinity had a significant effect on the nitrifier denitrification and abiotic effect. The correlation analysis showed that the total N2O production rate was significantly positively correlated with the content of total carbon (TC), soil organic carbon (SOC), NH4+-N and the ratio of C: N. There was only abiotic processes significantly affected by TC and SOC in the four N2O production processes. In order to decrease the production and emission of N2O in the coastal aquaculture ecosystem, the salinity of aquaculture ecosystem would be increased and the contents of organic carbon and inorganic nitrogen would be reduced by increasing the exchange frequency between aquaculture water and seawater.