The addition of silicon (Si) and organic fertilizers to soil conditioners can inhibit the transfer of heavy metal ions from soil to crops. However, it is not clear how Si and organic fertilizers affect soil properties and the micro-ecological environment and thereby reduce cadmium (Cd) accumulation in rice. In this study, the effects of L-type soil conditioners containing Si and organic fertilizers on bacterial and fungal community diversity, soil pH, organic matter, and available Si were analyzed with field experiments at two sites in Liuzhou City and Hezhou City, respectively, in Guangxi, China. With the increase of Si and organic fertilizer content in soil conditioner, rice yield respectively increased by 16.8–25.8 and 6.8–13.1%, and rice Cd content decreased significantly by 8.2–21.1 and 10.8–40.6%, respectively, at the two experimental sites. Soil microbiome analysis showed that the increase in abundance of Firmicutes and Actinobacteriota bacteria associated with Cd adsorption and sequestration, and Basidiomycota fungal populations associated with degradation of macromolecules favored the inhibition of soil Cd activity (soil exchangeable Cd decreased by 14.4–14.8 and 18.1–20.6%). This was associated with an increase in organic matter and Si content caused by applying soil conditioners. In conclusion, L-type soil conditioners, rich in Si and organic fertilizer, can reduce soil Cd bioavailability by regulating the dominant Cd passivating flora in the soil and ultimately reduce Cd accumulation in rice.