We used oat variety ‘Bayou 1’, which is susceptible to stem rust, as the experimental material, to study the effect of silicon application on the activity of proteases and phenolic substances in oat leaves infected with stem rust and to clarify the physiological mechanism of silicon improving resistance to oat stem rust, and provide theoretical basis for new control measures of oat stem rust. The results showed that: (1) after inoculation, the severity of oat stem rust was significantly reduced under silicon application, and the number of spores on leaves was significantly reduced. (2) No inoculation of stem rust, silicon application or not had no significant effect on the protease activity related to the disease course of oat leaves. The chitinase activity in the leaves increased rapidly and then decreased after reaching the peak on the 1st day and the 3rd day of inoculation; The β1,3 glucanase activity of leaves increased first and then decreased in both silicon and nonsilicon treatments, and reached the peak on the 3rd day of inoculation. The activities of chitinase and β1,3 glucanase in leaves were significantly increased after silicon application. (3) There was no significant effect of silicon application on the metabolism of phenolic substances in oat leaves without inoculation of stem rust, inoculation of stem rust could make oat leaves polyphenol oxidase activity (PPO), phenylalanine ammonia lyase activity (PAL), total soluble phenol content (TSP) and lignin content to increase rapidly. All treatments began to decline rapidly after reaching the peak on the 3rd day after inoculation, and application of silicon could significantly increase the content of each component in phenolic substances and related enzyme activities. In conclusion, silicon application can enhance the resistance of oat to stem rust by inducing the activity of protease related to disease course and the metabolism of phenolic substances in oat leaves.