The invention discloses a phosphorus and calcium type efficient and refined multiple-strain microbial organic fertilizer and a preparation method thereof, relating to the field of agricultural fertilizer. The microbial organic fertilizer is prepared by the following components in parts by weight: 44-54 parts of organic matter wastes, 10-15 parts of potassium chloride, 10-15 parts of humic acid, 0.4-0.6 part of intermediate trace elements, 0.4-0.6 part of microorganism, 5-10 parts of urea, 5-15 parts of superphosphate and 5-15 parts of diammonium phosphate (DAP) through the steps of mixing and pelletizing. The microbial organic fertilizer has the characteristics of good multi-bacteria symbiotic environment, stronger bioactivity, high fertilizer efficiency, full range of organic matters, effective micropopulation and chemical nutrients and controlled release effects. When in use, the phosphorus and calcium type efficient and refined multiple-strain microbial organic fertilizer in the invention can enhance the soil fertility, improve the fertilizer utilization rate, improve agricultural product quality, enhance plant diseases and insect pest resistance and drought resistance, inhibit crops from absorbing harmful substances such as heavy metals, pesticide and the like, purify and restore soil and the like, and is suitable for various crops and soils.