The aim of this study was to compare the free radical scavenging ability and intestinal epithelial cell protective effects of Java tea (Orthosiphon stamineus) root extracts (ORE), stem extracts (OSE), and leaf extracts (OLE) to determine the potential of Java tea by‐products. The Java tea extracts were prepared using a standard water–ethanol method. The antioxidant activity and intestinal protective effects were tested by H 2 O 2 ‐induced cell model and high‐fat diet‐induced mice model, respectively. The results showed that the total phenolic acid and flavonoid content and relative content were different in the ORE, OSE, and OLE. ORE had the highest total polyphenol and flavonoid content, the highest free radical scavenging rate, and the highest intracellular free radical scavenging rate. However, the yeast content in the ORE was lower than that in the OSE and OLE. All the Java tea extracts protected mouse intestine from high‐fat diet‐induced oxidative injury. This study indicates the potential of Java tea extracts as food or feed additives to protect the intestine from oxidative stress.