The invention discloses a straw-excrement microbial silage fertilizer and a preparation method thereof. The preparation method disclosed by the invention comprises the following steps: carrying out in-situ filamentation treatment on straws by adopting a straw filamentation machine to obtain straw filaments, and measuring the natural moisture content of the straw filaments; carrying out dry-wet separation and impurity removal treatment on the excrement to obtain dry excrement substances and wet excrement substances, and measuring the natural moisture content of the excrement; according to a preset fertilizer source material moisture content requirement and a preset burdening ratio requirement of the straw filaments dry matter and the excrement dry matter, determining the use amounts of thestraw filaments and the excrement in combination with the natural moisture content of the straw filaments and the natural moisture content of the excrement; respectively weighing the straw filaments and the excrement, and stirring and mixing the straw filaments and the excrement to obtain a fertilizer source material; spraying a microbial agent to the fertilizer source material, compressing the fertilizer source material into blocks according to a preset compression ratio, and briquetting and bagging the materials, and decomposing and fermenting the materials to obtain the straw-excrement micro-storage fertilizer. The method is easy to operate, the utilization rate of straw and excrement is increased, and resource waste and environmental pollution are reduced.