The invention discloses a biological organic silicon bacterial fertilizer capable of degrading heavy metals with high efficiency, and a preparation method thereof. The biological organic silicon bacterial fertilizer is prepared from a fermentation microorganism agent, a functional microorganism agent, an enzyme preparation, a rare earth silicon raw material, straw powder, an amino acid raw powder, abamectin residue, potassium fulvic acid, dioscorea zingiberensis residue, cassava residue, and livestock manure at a certain ratio. The preparation method comprises following steps: 1, cultivation of the activated fermentation microorganism agent; 2, cultivation of the activated functional microorganism agent; 3, fermentation preparation; 4, fermentation; and 5, fermentation postprocessing. The biological organic silicon bacterial fertilizer is capable of reducing heavy metal content of soil, providing plants with abundant trace elements, improving plant biological characters, resisting diseases and insects, and realizing nitrogen fixation, phosphorus dissolving, and potassium releasing. The preparation method is simple; operation is convenient; production cost is low; and the preparation method is suitable for popularization and industrialized large-scale production.