Summary The objective of this study was to investigate the effect of mixed kojis on essential indices of fish sauce. Fish sauce inoculated with mixed kojis ( FSB , Aspergillus oryzae koji: Aspergillus niger koji = 3:1) and A. oryzae koji ( FSA , control) was prepared. At the end of fermentation, the content of amino nitrogen, total soluble nitrogen, Free amino acid (FAA) and glutamic acid in FSB increased by 7.50%, 7.84%, 9.80% and 28.43% compared to FSA , due to higher acid protease activity in mixed kojis. Moreover, flavour groups including phenols, ketones and nitrogen‐containing compounds in FSB were also improved. According to the results of sensory evaluation, FSB showed higher intensity of umami and caramel attributes, lower intensity of ammonia and sour attributes. All the results suggested that the usage of mixed kojis to produce fish sauce was an effective method that can accelerate the fermentation process and improve the flavour of fish sauce made with freshwater fish by‐products.