The invention discloses a biological organic fertilizer suitable for organic agriculture as well as a preparation method and application of the biological organic fertilizer. The biological organic fertilizer comprises organic fertilizer raw materials, a decomposition agent accounting for 0.1-0.5% of the weight of the organic fertilizer raw materials, and a functional microbial agent accounting for 0.1-0.5% of the weight of the organic fertilizer raw materials. The organic fertilizer raw materials comprise the following raw materials in parts by weight: 8-12 parts of oil cake; 0.5-1 part of ground phosphate rock; 0.5-1 part of potassium feldspar; and 1-2 parts of humic acid. The biological organic fertilizer is applied to pea planting. When the biological organic fertilizer is used in the field of pea planting, growth and development of peas are promoted, the yield of the peas is increased, and economic benefits are improved. Meanwhile, the organic fertilizer disclosed by the invention can decompose insoluble phosphorus and potassium elements in soil, promote absorption and utilization of plants, increase the output value and improve the economic benefits.