The objective of this research was to investigate the impact of inoculating autochthonous starter cultures on the alterations in microorganisms, biogenic amines, nitrite, and N-nitrosamines in Chinese traditional fermented fish products (CTFPs) during in vitro human digestion. The results revealed that gastric digestion significantly (p < 0.05) inhibited the proliferation of lactic acid bacteria, yeast, Staphylococcus, and Enterobacteriaceae, whereas various microorganisms proliferated extensively during small intestine digestion. Meanwhile, small intestine digestion could significantly increase (p < 0.05) levels of putrescine, cadaverine, and tyramine. The reduced content observed in inoculated fermentation groups suggests that starter cultures may have the ability to deplete biogenic amines in this digestion stage. Gastric digestion significantly (p < 0.05) inhibited nitrite accumulation in all CTFPs samples. Conversely, the nitrite content increased significantly (p < 0.05) in all groups during subsequent small intestine digestion. However, the rise in the inoculated fermentation groups was smaller than that observed in the spontaneous fermentation group, indicating a potentially positive role of inoculated fermentation in inhibiting nitrite accumulation during this phase. Additionally, gastric digestion significantly (p < 0.05) elevated the levels of N-nitrosodimethylamine (NDMA) and N-nitrosopiperidine in CTFPs. Inoculation with L. plantarum 120, S. cerevisiae 2018, and mixed starter cultures (L. plantarum 120, S. cerevisiae 2018, and S. xylosus 135 [1:1:1]) effectively increased the degree of depletion of NDMA during this digestion process.