Biodegradable plastics, were considered environmentally friendly, may produce more microplastic particles (MPs) within the same period and exert more pronounced adverse effects on human health than traditional non-biodegradable plastics. Thus, this study investigated the changes of two kinds of biodegradable MPs from different sources in the digestive tract by using simulated digestion and fermentation models in vitro, with particle size, scanning electron microscopy (SEM) and gel permeation chromatography (GPC) analysis, and their implications on the gut microbiota were detected by full-length bacterial 16S rRNA gene amplicon sequencing. Poly(ε-caprolactone) (PCL) MPs exhibited stability in the upper gastrointestinal tract, while poly(lactic acid) (PLA) MPs were degraded beginning in the small intestine digestion phase. Both PCL and PLA MPs were degraded and oligomerized during colonic fermentation. Furthermore, this study highlighted the disturbance of the gut microbiota induced by MPs and their oligomers. PCL and PLA MPs significantly changed the composition and reduced the α-diversity of the gut microbiota. PCL and PLA MPs exhibited the same inhibitory effects on key probiotics such as Bifidobacterium, Lactobacillus, Faecalibacterium, Limosilactobacillus, Blautia, Romboutsia, and Ruminococcus, which highlighted the potential hazards of these materials for human health. In conclusion, this study illuminated the potential biodegradation of MPs through gastrointestinal digestion and the complex interplay between MPs and the gut microbiota. The degradable characteristic of biodegradable plastics may cause more MPs and greater harm to human health.