A field experimental were conducted in acid paddy soil to study the influence of the fermented rapeseed residue as an organic fertilizer on soil organic matter (OM), pH value, microbial biomass carbon and nitrogen (MBC and MBN), three enzymes (acid phosphatase, ACP, urease, UA, and dehydrogenase, DH), and occurrence mode of Cd in soil. Path analysis was used to study the influence approaches and mechanisms of organic fertilizer application on soil Cd occurrence mode. The results showed that:(1) The application of organic fertilizer could significantly increase the OM content, alleviate soil acidity, significantly increase the concentrations of reducible Cd (Red-Cd) and oxidizable-Cd, and decrease the concentrations of acid extractable-Cd (Aci-Cd) in soil. (2) ACP, UA and DH activities and MBC and MBN concentrations in soil were showed gradually raised after organic fertilizer application. (3) Path analysis results showed that the reduction of Aci-Cd concentrations in soil after organic fertilizer application was mainly achieved by increasing of OM content, DH activity, and MBC concentrations in soil. The decision coefficients of soil OM content, soil DH activity, and MBC content were 0.846, 0.257 and -0.276, respectively, which reached the significant levels and suggested they are the main controlling factors of soil Aci-Cd content under organic fertilizer application.