Brown rice noodles are recognized for their health benefits. While previous research has focused on improving noodle properties through various processing conditions, the effects on digestibility and fermentability remain unclear. This study comprehensively investigated how brown rice flour particle size influences noodle digestibility and gut microbiota fermentation in vitro. Particle size first affects flour properties. The average particle size of BR15 flour (62 μm) falls between the length and width of the endosperm cells, effectively disrupting the cell walls while minimizing excessive starch damage, thus achieving an optimal balance and resulting in the highest peak viscosity. As a result, brown rice noodles made from BR15 flour exhibited the lowest starch digestibility in vitro. X-ray diffraction analysis revealed that starch crystals in digestive residues were predominantly V-type, with BR15 showing the highest relative crystallinity. In vitro fecal fermentation indicated elevated Bifidobacterium abundance and butyrate production for BR15 noodles compared to others. The moderate particle size of BR15 brown rice flour imparts unique digestibility and gut microbiota modulation to the noodles produced. This study provides insights into particle size optimization for improving nutritional quality of brown rice noodles.