Inhibitory effect is one of the important factors causing the problem in continual watermelon mono-cropping system. The study was about the effects of main inhibitory substance-benzoic acid and cinnamic acid on radicle growth, microstructure and ultrastructure of watermelon. Benzoic acid and cinnamic acid significantly effected watermelon radicles elongation. With the increasing of benzoic acid and cinnamic acid concentration, the growth speed was decreased, and the radicles were short. Through the observation to the root tip microstructure and ultrastructure it was found that benzoic acid and cinnamic acid could result to root tip nuclei irregular, nucleolus abnormal, and cytoplasm sparse. Vacuoles became more and bigger. The Effects of benzoic acid treated on vacuoles was more significant than cinnamic acid treated. But to nucleolus, the effects of cinnamic acid treated was more significant than benzoic acid treated.