Heat stress induced by continuous high ambient temperatures or strenuous exercise in humans and animals leads to intestinal epithelial damage through the induction of intracellular stress response. However, the precise mechanisms involved in the regulation of intestinal epithelial cell injury, especially intestinal stem cells (ISCs), remain unclear. Thereby, in vitro a confluent monolayer of IPEC‐J2 cells was exposed to the high temperatures (39, 40, and 41°C), the IPEC‐J2 cell proliferation, apoptosis, differentiation, and barrier were determined, as well as the expression of GRP78, which is a marker protein of endoplasmic reticulum stress (ERS). The Wnt/β‐catenin pathway‐mediated regenerative response was validated using R‐spondin 1 (Rspo1). And ex‐vivo, three‐dimensional cultured enteroids were developed from piglet jejunal crypt and employed to assess the ISC activity under heat exposure. The results showed that exposure to 41°C for 72 hr, rather than 39°C and 40°C, decreased IPEC‐J2 cell viability, inhibited cell proliferation and differentiation, induced ERS and cell apoptosis, damaged barrier function and restricted the Wnt/β‐catenin pathway. Nevertheless, Wnt/β‐catenin reactivation via Rspo1 protects the intestinal epithelium from heat exposure‐induced injury. Furthermore, exposure to 41°C for 24 hr reduced ISC activity, stimulated crypt‐cell apoptosis, upregulated the expression of GRP78 and caspase‐3, and downregulated the expression of β‐catenin, Lgr5, Bmi1, Ki67, KRT20, ZO‐1, occludin, and claudin‐1. Taken together, we conclude that heat exposure induces ERS and downregulates the Wnt/β‐catenin signaling pathway to disrupt epithelial integrity by inhibiting the intestinal epithelial cell proliferation and stem cell expansion.