The invention provides an intermediate phosphorite separation method and system. According to the separation method, after crushing treatment, raw ores are mixed with water and ground, so that ore pulp is obtained, the ore pulp is screened into intermediate-particle-size ore pulp and primary coarse ore pulp, classification and sedimentation are conducted on the intermediate-particle-size ore pulp,then fine ore pulp and secondary coarseore pulp are obtained, the secondary coarse ore pulp and the primary coarse ore pulp are mixed and blended, and then obtained finished-product ore pulp is conveyed to each production workshop. The intermediate phosphorite separation system comprises a crushing treatment unit, a proportioning unit, an overflow ball mill A, a hydrocyclone A, a hydrocyclone B,an ore mixing and blending unit, an outputting unit and the like. By the adoption of the technical scheme, the appropriate device is adopted to conduct selective milling according to the difference ofthe mineral hardness of raw ores, acid non-soluble substances and silica gel can be easily enriched in the fine-grade ore powder, then classifying and selective ore milling are conducted, and the screened out coarse ore pulp and fine ore pulp can be both reasonably utilized; and, the utilization rate of intermediate phosphorite is improved, and the particle size difference of the ore powder is controlled.