The invention relates to a microbiological composite bacterial inoculum and a preparation method thereof, in particular to the microbiological composite bacterial inoculum used for preparing a biological bacterial fertilizer. The microbiological composite bacterial inoculum is prepared by culturing Rhodop seudanonas palustris, Candida utilis, Lactobacillus acidophilus, Bacillus subtilis and Streptomyces microflavus var. lactosus which are disclosed in a culture catalogue of the China Center for General Microbiology Culture Collection (CGMCC), wherein the serial number of the Rhodop seudanonaspalustris is 1.2352; the serial number of the Candida utilis is 2.1180; the serial number of the Lactobacillus acidophilus is 1.1854; the serial number of the Bacillus subtilis is 1.1630; the serial number of the Streptomyces microflavus var. lactosus is 4.0891; and the weight ratio of the Rhodop seudanonas palustris to the Candida utilis to the Lactobacillus acidophilus to the Bacillus subtilis is 1:0.5:0.5:0.1. When used for preparing the biological bacterial fertilizer, the composite bacterial inoculum can effectively decompose and release crude fibers and other nutrient components in straws and livestock manure; and the prepared biological organic fertilizer can condition the soil, increase the activity rate of microorganisms in the soil, avoid soil hardening, improve the permeabilityof the soil, play a role in production increasing, and effectively solve the problem of the area source pollution of agricultural wastes in rural areas.