Microbial metabolites regulate physiological functions and intestinal disease by shaping ISCs. Trp maintains ISC homeostasis through AhR. No matter whether Trp metabolites are generated by Trp‐metabolizing bacteria, or Kyn regulated by IDO from Trp, both regulate AhR by serving as AhR ligands and AhR receptor agonists, respectively. SCFAs are identified as ISC effectors. Butyrate, as an inhibitor of HDAC or a ligand for GPCRs, suppress ISC proliferation at physiologic concentrations. However, crypt structure and colonocytes can protect ISCs and progenitor cells to alleviate this effect. Endotoxin is present in the cell wall of Gram‐negative bacteria, which consists of LPS and peptidoglycan. LPS, acting on TLR4, can reduce the proliferation of Lgr5+ ISCs or organoids by regulating phosphorylation of Akt, Apc complex, and the Wnt signaling pathway. MDP, enhanced by peptidoglycan, induces proliferation of Lgr5+ ISCs and exerts cytoprotection via NOD‐2 and the followed NF‐κB. Bacterial anabolic products, including palmitic acid, activate Wnt signals by both PPARδ and TNF‐α. TNF‐α promotes GSK‐3β phosphorylation and inactivates the Apc complex, which is a negative regulator of Wnt signals. AhR, aryl hydrocarbon receptor; Akt, protein kinase B; Apc, adenomatosis polyposis coli; CK1, Casein kinase 1; c‐Myc, cellular Myc; GPR43, G protein‐coupled receptor 43; GSK‐3β, glycogen synthase kinase‐3 beta; HDAC, histone deacetylase; Hes1, hairy and enhancer of split 1; IDO, indoleamine 2,3‐dioxygenase; ISC, intestinal stem cell; Kyn, kynurenic acid; LPS, lipopolysaccharide; MDP, muramyl dipeptide; NF‐κB, nuclear factor kappa B; NOD, nucleotide‐binding oligomerization domain; PPARδ, peroxisome proliferator‐activated receptor δ; RNF43, Ring Finger Protein 43; SCFAs, short‐chain fatty acids; Tcf4, T‐cell factor 4; TDO, tryptophan‐2,3‐dioxygenase; TLR4, Toll‐like receptor 4; TNF‐α, tumor necrosis factor alpha; Trp, tryptophan; ZNRF3, Zinc And Ring Finger 3.