Honokiol, as a pharmacological active small-molecule, has received significant attention for its strong pharmacological effects without remarkable toxicity. However, the metabolites of honokiol in the small intestine, one of the most important extrahepatic sites of drug biotransformation, are unknown. In this article, a method of ¹³C stable isotope labeling followed by ultra-high performance liquid chromatography/quadrupole time-of-flight tandem mass spectrometry (UHPLC/Q-TOF-MS) was applied to identify the metabolites of honokiol in rat small intestines. According to the unique isotopic patterns of two peaks with similar intensities and a ratio of nearly 1 : 1, and molecular weight difference of 6 Da between honokiol and ¹³C-labeled honokiol, a total of 20 metabolites were observed and tentatively characterized in the small intestine. Eight of these were reported for the first time. All of them were phase II metabolites and divided into sulfates, amino acid conjugates and glucuronide metabolites. This study, combined with a previously reported paper about honokiol metabolites in rat feces, plasma and urine, will benefit further studies of the metabolism and mechanism of action of honokiol in vivo.