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In this study, the digestion of pectic polysaccharide from Brassica rapa L. (BRP) in vitro and its effect on the intestinal microbiota in cyclophosphamide (Cy)‐treated mice were investigated. As a result, the molecular weight (Mw) of BRP was significantly decreased after simulated gastrointestinal digestion, and content of reducing sugars (CR) was significantly increased (P < 0.05), implying that BRP was gradually degraded under gastrointestinal digestion conditions in vitro. In vivo, both 50 or 200 mg kg−1·BW/d of BRP significantly improved SCFAs concentrations that decreased by Cy treatment (P < 0.05). Meanwhile, BRP enriched the alpha‐diversity of intestinal microbiota and altered the microbial composition with an increase of Lactobacillus and a decrease of Clostridium, Ruminococcus, Oscillospira (P < 0.05). Besides, BRP intervention was conducive to the recovery of mouse body weight, thymus and spleen indices, and contributed to improve the intestinal barrier. [ABSTRACT FROM AUTHOR]