Trimethylamine oxide (TMAO), a microbial metabolite commonly found in foods, has been attracting increasing attention as it is associated with the risk of several diseases. Simple and accurate analytical methods are crucial for TMAO study. In the present study, we proposed a chemical reaction‐based fluorescence assay for TMAO detection using synthetic small molecular probes. After systematic screening and optimization, the sensitive and selective quantification of TMAO has been achieved based on a fluorescence probe P6 (3‐iodopropanyl group modified resorufin). Excellent linearity (R2 = 0.997) was found between 6.25 and 50 μM, and the limit of detection (LOD) was 0.20 μM. Using this method, TMAO levels in several marine fishes and shellfishes have been successfully analyzed. The probe‐based assay offers a simple and useful way for TMAO determination. The design is inspired by the unique oxidation reaction between TMAO and halogen, which opens a new perspective in the development of more advanced analytical assays for TMAO in the future.