The invention provides a composite active bacterial preparation which is used for aquatic products and has the water improving and fertilizing functions and a preparation method thereof by applying a modern bioengineering technology mainly for the problem that in existing aquaculture, the water quality of a pond is poor. The composite microecological preparation is prepared by mixing bacillus subtilis, bacillus megatherium, bacillus amyloliquefaciens, bacillus licheniformis, enterococcus faecium, lactobacillus brevis, lactobacillus plantarum, lactococcus lactis and saccharomyces cerevisiae through liquid-submerged fermentation. In the liquid preparation, microorganisms are in a dormant state and are stable and easy to preserve, after the preparation is put into water, the dormant strains can quickly resuscitate, harmful substances such as nitrite nitrogen and ammonia nitrogen in the water are quickly decomposed, good algae growth is facilitated, harmful algae reproduction is inhibited, and therefore the purpose of improving the water quality of the culture water is achieved.