Seedlings blight is one of the destructive diseases of rice, caused by the fungus Fusarium oxysporum, which impairs rice productions. Fluoro-substituted benzothiadiazole derivatives (FBT) and chitosan oligosaccharide (COS) are elicitors that can enhance plant resistance to pathogen infection. However, there is a lack of information regarding FBT and COS used as elicitors in rice seedlings blight. Therefore, the aim of this study was to evaluate the effect of FBT and COS treatments against rice seedling blight and elucidate the possible molecular mechanisms of the two elicitors for inducing resistance by proteomics. The results showed that FBT and COS significantly reduced the disease incidence and index, and improved the growth status of rice root caused by F. oxysporum. Biochemical analysis demonstrated that the two elicitors effectively enhanced activities of defense enzymes. Moreover, proteomic profiling analysis of rice root tissues disclosed more differentially expressed proteins in diterpenoid biosynthesis pathway induced by the two elicitors compared with other biological pathways, resulting in the accumulation of antimicrobial substance--momilactone. This study provided the basis of theory and application for FBT and COS used as rice elicitors against seedling blight on roots.