The invention discloses a Pseudomonas fluorescens Y13, and a preparation method and applications thereof. The preparation method comprises the following steps: 1, weighing a soil sample, putting in disinfected normal saline, oscillating on a constant temperature shaking table, and allowing an obtained solution to stand; 2, taking an obtained supernatant to a Mengjinna organophosphorus liquid medium; 3, culturing on the constant temperature shaking table, inoculating to a fresh organophosphorus liquid medium, and continuously culturing; 4, coating an organophosphorus solid flat with different dilution ratios of a dilution, inverting in a constant temperature culture box, and culturing; and 5, purifying single colonies obtained on the flat, and preserving a finally obtained pure culture on an LB inclined plane. An above obtained strain is identified as Pseudomonas fluorescens Y13, is preserved and has a preservation number of CCTCC NO:M2012121. The Pseudomonas fluorescens Y13 has the advantages of easy preparation obtaining, low cost, increase of the content of soluble phosphorus in soil, substantial promotion of the phosphorus element absorption and utilization of plants, high yield of crops, reduction of the planting cost and the agricultural investment, and alleviation of the environmental pollution caused by the excess application of an agricultural phosphorus fertilizer.