Sauerkraut is a unique traditional fermented food in Northeast China and it produces biogenic amines, a potential hazard compound, due to its complex microbial metabolic process during fermentation. Therefore, the relationship between bacterial diversity and biogenic amines in naturally fermented sauerkraut collected from different regions in Northeast China was investigated. There were significant differences in content of total acid, nitrite, salt, reducing sugar, free amino acid, and biogenic amine, total number of colonies and total number of lactic acid bacteria in sauerkraut samples from 6 regions. The total number of colonies, total number of lactic acid bacteria and biogenic amine content ranged from 5.11~5.81 lg CFU/g, 4.09~5.12 lg CFU/g, 59.22~131.34mg/kg, respectively. The composition of bacterial community structure in natural fermented Northeast sauerkraut was analyzed by high-throughput sequencing analysis technology. The results showed that the dominant bacteria in sauerkraut mainly included Lactobacillus and Pseudarcobacter. Spearman correlation analysis showed that, among the top ten bacterial genera of relative abundance, there was a significant positive correlation between Insolitispirillum and the content of cadaverine(P<0.05) and a significant negative correlation between Insolitispirillum and the content of histamine(P<0.01). Arcobacter was significantly negatively correlated with the content of spermine(P<0.05). Comamonas was significantly positive correlated with the content of spermine(P<0.05). Pediococcus was significantly positive correlated with the content of tyramine(P<0.01). Insolitispirillum and Pseudarcobacter were significantly negatively correlated with the content of tyramine(P<0.05). Prevotella was significantly negatively correlated with the content of spermine(P<0.01). Therefore, in subsequent research, strains that are negatively correlated with biogenic amines could be isolated and purified as functional fermentation agents to inhibit the production and accumulation of biogenic amines in fermented vegetables. This study aimed to provide a theoretical basis for understanding the formation rule and mechanism of biogenic amines production, effectively controlling biogenic amines, and improving the quality and safety of naturally fermented sauerkraut.