Ferulate-5-hydroxylase (F5H) is a key enzyme involved in the conversion of the guaiacyl monolignol (G-monolignol) to the syringyl monolignol (S-monolignol) in angiosperms. The monolignol ratio has been proposed to affect biomass recalcitrance and the resistance to plant disease. Sclerotinia sclerotiorum (S. sclerotiorum) stem rot of Brassica napus (B. napus) causes heavy damage in oilseed rape production. To date, there is no information about the effect of the lignin monomer ratio on the resistance to S. sclerotiorum in B. napus. Four dominantly expressed BnF5H genes were knocked out by CRISPR/Cas9 simultaneously in B. napus, and the f5h mutant KO-7 was generated. The S/G lignin composition ratio was decreased compared to that of the wild type (WT) based on the results of Mӓule staining and 2D-NMR profiling. The resistance to S. sclerotiorum in stems and leaves increased in KO-7. Furthermore, we found that the stem strength of KO-7 was significantly increased compared to that of the WT. Collectively, for the first time, we demonstrate that knockout of the lignin pathway gene F5H decreases the S/G ratio, improves S. sclerotiorum resistance in B. napus, and increases stem strength.