Fungi, as an important microorganism in sauerkraut, have not been revealed in depth concerning sauerkraut safety and quality. Therefore, this study aimed to evaluate the fungal communities, safety, and quality properties of 27 traditional fermented sauerkrauts collected from nine different regions in Northeast China. The results revealed that Debaryomyces, Candida, Pichia, Dipodascus, Naumovozyma, Kazachstania, Cutaneotrichosporon, Tausonia, Wickerhamomyces, and IssatchenkiaIt were the dominant fungus, at the genus level, of northeastern sauerkraut. SH1 (16.60 ± 0.07 mg/kg) and QQHR1 (233.59 ± 2.85 mg/kg) had the highest nitrite and biogenic amine contents, respectively (P < 0.05). Five fungi at the genus level (Kazachstania, Pichia, Wickerhamomyces, Dipodascus, and Candida) were significantly correlated with biogenic amines (BAs). Additionally, four fungi (Tausonia, Wickerhamomyces, Dipodascus, and Candida) were significantly correlated with flavor formation in northeastern sauerkraut. Candida was considered the most important core fungus, as it had the most significant positive correlation with BAs and quality properties of northeastern sauerkraut. This study revealed the contribution of fungi to improving the safety and quality of northeastern sauerkraut.