Water quality management is important in cage culture of the Asian swamp eel (Monopterus albus). However, it is difficult to manage water quality after a large number of eels have died within the cages. The present study seeks to solve this problem by establishing a method to judge and maintain water quality. To this end, the effect of temperature and eel body weight on the water quality and microorganisms after the death of Asian swamp eels have been examined in the laboratory. The results showed that the changes in water quality parameters were similar at different temperatures and different eel weights. For example, at 26°C, the water quality started deteriorating at 5–7 days after death, which corresponded to the oxygen consumption stage. This was followed by the anaerobic decomposition stage at 11 days after death, at which point the self-purification process of the water body was initiated. Under a lower temperature of 18°C, the oxygen consumption stage and, therefore, the overall decomposition process were extended. Proteobacteria, Bacteroidetes and Verrucomicrobia were the dominant phyla detected during the decomposition process, but the relative proportions of the dominant families differed across the stages. Based on these findings, we have provided innovative suggestions for water quality detection and management in Asian swamp eel production: (i) at a water temperature of 16–23°C, the following measures should be taken to deal with dead eels 15 days after the introduction of seedlings: (a) at an ammonia nitrogen level higher than 2 mg/L, the bodies present at the bottom of the cage need to be fished out with a net. However, when the ammonia nitrogen level is not higher than 2 mg/L, the whole cage should be sprayed with detoxifying substrate improver or Bacillus powder, according to the instructions, to improve water quality. (ii) At a water temperature of 23–30°C, the above measures should be taken on the 6th day after the seedlings are released, provided the critical value of ammonia nitrogen is 1.57 mg/L. An important limitation of this study is that water exchange was not possible under the laboratory experimental conditions, and the deterioration of water quality caused by eel death may have been alleviated due to water exchange between the inside and outside of the cage.