Not only is solving freshwater resource shortages effective but also an important measure for realizing the sustainable development of agriculture through the development and use of unconventional water resources. This pot experiment investigated the role of exogenous silicon in the risk of secondary soil salinization and the growth physiology of Lvxiu pakchoi cabbage under irrigation by using brackish water alone (BW), reclaimed water alone (RW), and compound irrigation with brackish water and reclaimed water at a ratio of 1:1, as well as the distribution of silicon in a soil–crop system. The results showed that with the extension of the spraying period of silicon fertilizer, the electrical conductivity (EC) decreased under 1:1 compound irrigation. The pH values in all treatments ranged from 7.95 to 8.10 without a potential risk of alkalization. Spraying silicon fertilizer had a positive effect on increasing the ratio of exchangeable potassium to sodium in soil. Spraying silicon fertilizer significantly reduced the percentage of exchangeable sodium (ESP) and the sodium adsorption ratio (SAR) in soils irrigated using BW, and increased the soil ESP and SAR under compound irrigation and RW irrigation, but these factors did not exceed the threshold of soil salinization. The proper application of silicon fertilizer had no significant effect on the total silicon content in the soil but increased the total silicon content in the plants to some extent. In addition, the yield was improved through proper silicon fertilizer application. In summary, exogenous silicon has positive effects on soil physical and chemical properties and crop growth, and relieves secondary salinization risk under compound irrigation via brackish water and reclaimed water.