Traditional methods of seed viability evaluation based on germination or detecting physiological indicators have several disadvantages, such as time consumption, seed destruction, and skill requirements et al. In this study, a nondestructive method based on surface desorption atmospheric pressure chemical ionization mass spectrometry (DAPCI–MS) was developed to evaluate radish [Raphanus sativus (L.) Domin] seed viability by detecting the sinapine that leakage from the interior of the seed to the coat. The signal intensity of the detected sinapine in seed coat by DAPCI–MS was significantly negatively correlated with the seed viability. One seed could be analyzed in an average of 4.4 s. We establish a new method to test radish seed viability based on DAPCI‐MS. This is a highly sensitive and high‐throughput method for detection without sample pretreatment. In addition, this study also provides new insights into the evaluation of seed viability in other plants.