In this study， high-throughput sequencing was used to analyze the changes of bacterial community structure during fermentation of stinky mandarin fish， and PICRUSt was used to predict the metabolic function of bacterial community. The results showed that the bacterial community of stinky mandarin fish was mainly consists of Muribaculaceae， Burkholderia-Caballeronia-Paraburkholderia， Lactobacillus， Psychrophilic， Pantobacterium， Hafnia-Obesumbacterium， Citrobacillus， Serratia， etc. Based on OTU level， the samples of stinky mandarin fish could be clustered into three fermented stages including early stage (0-2 d)， middle stage (4-8 d) and late stage (10-16 d). The abundance of dominant bacteria at the middle and late stages of fermentation were higher than those at the early stages of fermentation. Lactobacillus occupied absolute advantage at the middle and late stages of fermentation， mostly of Lactobacillus sakei with the largest relative abundance of 43.43%， and played an important role during the formation of flavor quality in stinky mandarin fish. PICRUSt analysis showed that the bacterial community function in the fermentation system of stinky mandarin fish mainly focused on amino acid transport and metabolism， carbohydrate transport and metabolism， and the functional composition of samples at different fermentation stages was relatively similar. This study aimed to provide theoretical basis for the development and application of microbial resources of stinky mandarin fish by studying the changes of bacterial community structure and metabolic functions during its fermentation process.