The invention discloses a composite micro-ecological preparation for treating black stink water in rivers, pits and ponds and a preparation method thereof. The composite microbial preparation comprises indigenous microorganism, functional strain and carrier matrix which are separated from a black stink water body to be treated and have a repairing function. The indigenous microorganism is at leastone of nitrifying bacteria, denitrifying bacteria and bacillus subtilis, the functional strain is at least one of photosynthetic bacteria, candida utilis, bacillus megaterium, lactic acid bacteria and actinomycetes, and the carrier matrix is at least one of crocalite, green zeolite, ceramsite, quartz sand, vesuvianite and vermiculite. The black stink water body includes black stink surface waterof black stink rivers, black stink lakes or polluted ground. According to the invention, the composite micro-ecological preparation is formed by immobilizing the indigenous microorganism, the functional strain and the carrier matrix, has remarkable effects of degrading the pollutants such as COD, NH3-N, TP and the like in the black stink water. The preparation method disclosed by the invention haswide applicability to black stink surface water of various black stink rivers, black stink lakes or polluted ground.