The invention relates to a composite micro-ecological water quality regulator and a preparation method thereof. The regulator is prepared from, by weight, 1-1.2% of vitamin A, 1-1.2% of vitamin B2, 0.5-0.8% of vitamin B6, 10-15% of vitamin C, 4-8% of taurine and 73.8-83.5% of glucose. In the regulator, the content concentration of mixed bacteria is 107-109 CFU / g. During preparation, firstly, EM, bacillus licheniformis and bifidobacterium are prepared into a fermentation seed solution, then fermentation liquor is prepared, and lastly the mixed fermentation liquor, vitamin A, vitamin B2, vitamin B6, vitamin C, taurine and glucose are subjected to mixing granulation, and the regulator is prepared. The preparation method is simple, the steps are easy to operate, the prepared regulator is suitable for aquaculture of all marine and freshwater varieties such as finless eels, loaches, fishes, shrimps, crabs and sea cucumbers, aquaculture water can be restored quickly, the physique and anti-stress ability of bred animals are enhanced, the survival rate of fry is increased, digestion is promoted, absorption is guaranteed, the yield of the bred animals is raised, and the quality of the bred animals is improved.