[Objectives] To investigate the application effect of compound microbial fertilizer on crops. [Methods] Livestock and poultry breeding waste, rapeseed cake and peanut straw were fully decomposed, and then added with compound functional microbial inoculum to produce Aisi Si/TE (active chelated silicon/trace element) compound microbial fertilizer, which was used to conduct 10% nitrogen reduction alternative fertilization experiment on rice. [Results] The yield of rice applied with 225 kg/ha Aisi Si/TE compound bacterial fertilizer was 7 203 kg/ha, increased by 5.4%, 6.9% and 46.9%, respectively compared to those of rice applied with 225 kg/ha inactivated Aisi Si/TE compound microbial fertilizer, conventional fertilization and blank control (P<0.01). Application of Aisi Si/TE compound microbial fertilizer to rice improved soil organic matter and effective nutrient content and showed obvious effect of saving nitrogen and increasing yield and income. In addition, it provided a good micro-ecological environment, passivated and solidified heavy metals, effectively reduced the biological mobility of heavy metals, and greatly reduced the cadmium content in rice. [Conclusions] Application of Aisi Si/TE compound microbial fertilizer is beneficial to improving the quality of agricultural products.